sashimi_plot: sashimi-plot.py annotate

author	artbio
date	Fri, 23 Aug 2019 11:38:29 -0400
parents
children

rev	line source
0 9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	1 #!/usr/bin/env python
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	2
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	3 # Import modules
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	4 import copy
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	5 import os
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	6 import re
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	7 import subprocess as sp
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	8 import sys
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	9 from argparse import ArgumentParser
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	10 from collections import OrderedDict
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	11
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	12
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	13 def define_options():
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	14 # Argument parsing
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	15 parser = ArgumentParser(description="""Create sashimi plot for a given
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	16 genomic region""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	17 parser.add_argument("-b", "--bam", type=str,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	18 help="""
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	19 Individual bam file or file with a list of bam files.
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	20 In the case of a list of files the format is tsv:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	21 1col: id for bam file,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	22 2col: path of bam file,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	23 3+col: additional columns
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	24 """)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	25 parser.add_argument("-c", "--coordinates", type=str,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	26 help="Genomic region. Format: chr:start-end (1-based)")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	27 parser.add_argument("-o", "--out-prefix", type=str, dest="out_prefix",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	28 default="sashimi",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	29 help="Prefix for plot file name [default=%(default)s]")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	30 parser.add_argument("-S", "--out-strand", type=str, dest="out_strand",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	31 default="both", help="""Only for --strand other than
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	32 'NONE'. Choose which signal strand to plot:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	33 <both> <plus> <minus> [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	34 parser.add_argument("-M", "--min-coverage", type=int, default=1,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	35 dest="min_coverage", help="""Minimum number of reads
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	36 supporting a junction to be drawn [default=1]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	37 parser.add_argument("-j", "--junctions-bed", type=str, default="",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	38 dest="junctions_bed", help="""Junction BED file name
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	39 [default=no junction file]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	40 parser.add_argument("-g", "--gtf",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	41 help="Gtf file with annotation (only exons is enough)")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	42 parser.add_argument("-s", "--strand", default="NONE", type=str,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	43 help="""Strand specificity: <NONE> <SENSE> <ANTISENSE>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	44 <MATE1_SENSE> <MATE2_SENSE> [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	45 parser.add_argument("--shrink", action="store_true",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	46 help="""Shrink the junctions by a factor for nicer
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	47 display [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	48 parser.add_argument("-O", "--overlay", type=int,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	49 help="Index of column with overlay levels (1-based)")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	50 parser.add_argument("-A", "--aggr", type=str, default="",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	51 help="""Aggregate function for overlay:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	52 <mean> <median> <mean_j> <median_j>.
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	53 Use mean_j \| median_j to keep density overlay but
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	54 aggregate junction counts [default=no aggregation]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	55 parser.add_argument("-C", "--color-factor", type=int, dest="color_factor",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	56 help="Index of column with color levels (1-based)")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	57 parser.add_argument("--alpha", type=float, default=0.5,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	58 help="""Transparency level for density histogram
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	59 [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	60 parser.add_argument("-P", "--palette", type=str,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	61 help="""Color palette file. tsv file with >=1 columns,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	62 where the color is the first column""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	63 parser.add_argument("-L", "--labels", type=int, dest="labels", default=1,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	64 help="""Index of column with labels (1-based)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	65 [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	66 parser.add_argument("--height", type=float, default=2,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	67 help="""Height of the individual signal plot in inches
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	68 [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	69 parser.add_argument("--ann-height", type=float, default=1.5,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	70 dest="ann_height", help="""Height of annotation plot in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	71 inches [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	72 parser.add_argument("--width", type=float, default=10,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	73 help="""Width of the plot in inches
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	74 [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	75 parser.add_argument("--base-size", type=float, default=14,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	76 dest="base_size", help="""Base font size of the plot in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	77 pch [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	78 parser.add_argument("-F", "--out-format", type=str, default="pdf",
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	79 dest="out_format", help="""Output file format:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	80 <pdf> <svg> <png> <jpeg> <tiff>
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	81 [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	82 parser.add_argument("-R", "--out-resolution", type=int, default=300,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	83 dest="out_resolution", help="""Output file resolution in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	84 PPI (pixels per inch). Applies only to raster output
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	85 formats [default=%(default)s]""")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	86 return parser
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	87
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	88
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	89 def parse_coordinates(c):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	90 c = c.replace(",", "")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	91 chr = c.split(":")[0]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	92 start, end = c.split(":")[1].split("-")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	93 # Convert to 0-based
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	94 start, end = int(start) - 1, int(end)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	95 return chr, start, end
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	96
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	97
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	98 def count_operator(CIGAR_op, CIGAR_len, pos, start, end, a, junctions):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	99
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	100 # Match
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	101 if CIGAR_op == "M":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	102 for i in range(pos, pos + CIGAR_len):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	103 if i < start or i >= end:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	104 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	105 ind = i - start
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	106 a[ind] += 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	107
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	108 # Insertion or Soft-clip
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	109 if CIGAR_op == "I" or CIGAR_op == "S":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	110 return pos
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	111
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	112 # Deletion
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	113 if CIGAR_op == "D":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	114 pass
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	115
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	116 # Junction
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	117 if CIGAR_op == "N":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	118 don = pos
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	119 acc = pos + CIGAR_len
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	120 if don > start and acc < end:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	121 junctions[(don, acc)] = junctions.setdefault((don, acc), 0) + 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	122
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	123 pos = pos + CIGAR_len
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	124
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	125 return pos
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	126
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	127
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	128 def flip_read(s, samflag):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	129 if s == "NONE" or s == "SENSE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	130 return 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	131 if s == "ANTISENSE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	132 return 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	133 if s == "MATE1_SENSE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	134 if int(samflag) & 64:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	135 return 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	136 if int(samflag) & 128:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	137 return 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	138 if s == "MATE2_SENSE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	139 if int(samflag) & 64:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	140 return 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	141 if int(samflag) & 128:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	142 return 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	143
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	144
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	145 def read_bam(f, c, s):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	146
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	147 _, start, end = parse_coordinates(c)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	148
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	149 # Initialize coverage array and junction dict
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	150 a = {"+": [0] * (end - start)}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	151 junctions = {"+": OrderedDict()}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	152 if s != "NONE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	153 a["-"] = [0] * (end - start)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	154 junctions["-"] = OrderedDict()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	155
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	156 p = sp.Popen("samtools view %s %s " % (f, c), shell=True, stdout=sp.PIPE)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	157 for line in p.communicate()[0].decode('utf8').strip().split("\n"):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	158
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	159 if line == "":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	160 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	161
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	162 line_sp = line.strip().split("\t")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	163 samflag, read_start, CIGAR = line_sp[1], int(line_sp[3]), line_sp[5]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	164
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	165 # Ignore reads with more exotic CIGAR operators
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	166 if any(map(lambda x: x in CIGAR, ["H", "P", "X", "="])):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	167 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	168
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	169 read_strand = ["+", "-"][flip_read(s, samflag) ^ bool(int(samflag) &
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	170 16)]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	171 if s == "NONE":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	172 read_strand = "+"
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	173
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	174 CIGAR_lens = re.split("[MIDNS]", CIGAR)[:-1]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	175 CIGAR_ops = re.split("[0-9]+", CIGAR)[1:]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	176
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	177 pos = read_start
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	178
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	179 for n, CIGAR_op in enumerate(CIGAR_ops):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	180 CIGAR_len = int(CIGAR_lens[n])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	181 pos = count_operator(CIGAR_op, CIGAR_len, pos, start, end,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	182 a[read_strand], junctions[read_strand])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	183
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	184 p.stdout.close()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	185 return a, junctions
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	186
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	187
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	188 def get_bam_path(index, path):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	189 if os.path.isabs(path):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	190 return path
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	191 base_dir = os.path.dirname(index)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	192 return os.path.join(base_dir, path)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	193
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	194
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	195 def read_bam_input(f, overlay, color, label):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	196 if f.endswith(".bam"):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	197 bn = f.strip().split("/")[-1].strip(".bam")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	198 yield bn, f, None, None, bn
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	199 return
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	200 with open(f) as openf:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	201 for line in openf:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	202 line_sp = line.strip().split("\t")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	203 bam = get_bam_path(f, line_sp[1])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	204 overlay_level = line_sp[overlay-1] if overlay else None
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	205 color_level = line_sp[color-1] if color else None
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	206 label_text = line_sp[label-1] if label else None
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	207 yield line_sp[0], bam, overlay_level, color_level, label_text
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	208
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	209
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	210 def prepare_for_R(a, junctions, c, m):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	211
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	212 _, start, _ = parse_coordinates(args.coordinates)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	213
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	214 # Convert the array index to genomic coordinates
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	215 x = list(i+start for i in range(len(a)))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	216 y = a
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	217
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	218 # Arrays for R
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	219 dons, accs, yd, ya, counts = [], [], [], [], []
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	220
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	221 # Prepare arrays for junctions (which will be the arcs)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	222 for (don, acc), n in junctions.items():
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	223
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	224 # Do not add junctions with less than defined coverage
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	225 if n < m:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	226 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	227
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	228 dons.append(don)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	229 accs.append(acc)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	230 counts.append(n)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	231
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	232 yd.append(a[don - start - 1])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	233 ya.append(a[acc - start + 1])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	234
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	235 return x, y, dons, accs, yd, ya, counts
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	236
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	237
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	238 def intersect_introns(data):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	239 data = sorted(data)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	240 it = iter(data)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	241 a, b = next(it)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	242 for c, d in it:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	243 if b > c:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	244 # Use `if b > c` if you want (1,2), (2,3) not to be
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	245 # treated as intersection.
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	246 b = min(b, d)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	247 a = max(a, c)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	248 else:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	249 yield a, b
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	250 a, b = c, d
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	251 yield a, b
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	252
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	253
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	254 def shrink_density(x, y, introns):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	255 new_x, new_y = [], []
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	256 shift = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	257 start = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	258 # introns are already sorted by coordinates
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	259 for a, b in introns:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	260 end = x.index(a)+1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	261 new_x += [int(i-shift) for i in x[start:end]]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	262 new_y += y[start:end]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	263 start = x.index(b)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	264 L = (b-a)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	265 shift += L-L**0.7
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	266 new_x += [int(i-shift) for i in x[start:]]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	267 new_y += y[start:]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	268 return new_x, new_y
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	269
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	270
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	271 def shrink_junctions(dons, accs, introns):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	272 new_dons, new_accs = [0]len(dons), [0]len(accs)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	273 shift_acc = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	274 shift_don = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	275 s = set()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	276 junctions = list(zip(dons, accs))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	277 for a, b in introns:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	278 L = b - a
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	279 shift_acc += L-int(L**0.7)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	280 for i, (don, acc) in enumerate(junctions):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	281 if a >= don and b <= acc:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	282 if (don, acc) not in s:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	283 new_dons[i] = don - shift_don
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	284 new_accs[i] = acc - shift_acc
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	285 else:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	286 new_accs[i] = acc - shift_acc
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	287 s.add((don, acc))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	288 shift_don = shift_acc
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	289 return new_dons, new_accs
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	290
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	291
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	292 def read_palette(f):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	293 palette = "#ff0000", "#00ff00", "#0000ff", "#000000"
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	294 if f:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	295 with open(f) as openf:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	296 palette = list(line.split("\t")[0].strip() for line in openf)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	297 return palette
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	298
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	299
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	300 def read_gtf(f, c):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	301 exons = OrderedDict()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	302 transcripts = OrderedDict()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	303 chr, start, end = parse_coordinates(c)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	304 end = end - 1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	305 with open(f) as openf:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	306 for line in openf:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	307 if line.startswith("#"):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	308 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	309 (el_chr, _, el, el_start, el_end, _,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	310 strand, _, tags) = line.strip().split("\t")
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	311 if el_chr != chr:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	312 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	313 d = dict(kv.strip().split(" ") for kv in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	314 tags.strip(";").split("; "))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	315 transcript_id = d["transcript_id"]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	316 el_start, el_end = int(el_start) - 1, int(el_end)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	317 strand = '"' + strand + '"'
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	318 if el == "transcript":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	319 if (el_end > start and el_start < end):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	320 transcripts[transcript_id] = (max(start, el_start),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	321 min(end, el_end),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	322 strand)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	323 continue
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	324 if el == "exon":
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	325 if (start < el_start < end or start < el_end < end):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	326 exons.setdefault(transcript_id,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	327 []).append((max(el_start, start),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	328 min(end, el_end), strand))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	329
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	330 return transcripts, exons
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	331
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	332
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	333 def make_introns(transcripts, exons, intersected_introns=None):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	334 new_transcripts = copy.deepcopy(transcripts)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	335 new_exons = copy.deepcopy(exons)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	336 introns = OrderedDict()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	337 if intersected_introns:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	338 for tx, (tx_start, tx_end, strand) in new_transcripts.items():
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	339 total_shift = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	340 for a, b in intersected_introns:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	341 L = b - a
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	342 shift = L - int(L**0.7)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	343 total_shift += shift
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	344 for i, (exon_start, exon_end, strand) in \
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	345 enumerate(exons.get(tx, [])):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	346 new_exon_start, new_exon_end = new_exons[tx][i][:2]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	347 if a < exon_start:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	348 if b > exon_end:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	349 if i == len(exons[tx])-1:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	350 total_shift = total_shift - shift + \
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	351 (exon_start - a)(1-int(L*-0.3))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	352 shift = (exon_start - a)(1-int(L*-0.3))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	353 new_exon_end = new_exons[tx][i][1] - shift
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	354 new_exon_start = new_exons[tx][i][0] - shift
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	355 if b <= exon_end:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	356 new_exon_end = new_exons[tx][i][1] - shift
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	357 new_exons[tx][i] = (new_exon_start, new_exon_end, strand)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	358 tx_start = min(tx_start,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	359 sorted(new_exons.get(tx, [[sys.maxsize]]))[0][0])
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	360 new_transcripts[tx] = (tx_start, tx_end - total_shift, strand)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	361
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	362 for tx, (tx_start, tx_end, strand) in new_transcripts.items():
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	363 intron_start = tx_start
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	364 ex_end = 0
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	365 for ex_start, ex_end, strand in sorted(new_exons.get(tx, [])):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	366 intron_end = ex_start
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	367 if tx_start < ex_start:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	368 introns.setdefault(tx, []).append((intron_start, intron_end,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	369 strand))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	370 intron_start = ex_end
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	371 if tx_end > ex_end:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	372 introns.setdefault(tx, []).append((intron_start, tx_end, strand))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	373 d = {'transcripts': new_transcripts,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	374 'exons': new_exons,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	375 'introns': introns}
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	376 return d
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	377
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	378
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	379 def gtf_for_ggplot(annotation, start, end, arrow_bins):
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	380 arrow_space = int((end - start)/arrow_bins)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	381 s = """
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	382
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	383 # data table with exons
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	384 ann_list = list(
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	385 "exons" = data.table(),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	386 "introns" = data.table()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	387 )
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	388 """
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	389
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	390 if annotation["exons"]:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	391
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	392 s += """
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	393 ann_list[['exons']] = data.table(
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	394 tx = rep(c(%(tx_exons)s), c(%(n_exons)s)),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	395 start = c(%(exon_start)s),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	396 end = c(%(exon_end)s),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	397 strand = c(%(strand)s)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	398 )
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	399 """ % ({
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	400 "tx_exons": ",".join(annotation["exons"].keys()),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	401 "n_exons": ",".join(map(str, map(len,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	402 annotation["exons"].values()))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	403 "exon_start": ",".join(map(str, (v[0] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	404 annotation["exons"].values() for v in vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	405 "exon_end": ",".join(map(str, (v[1] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	406 annotation["exons"].values() for v in vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	407 "strand": ",".join(map(str, (v[2] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	408 annotation["exons"].values() for v in vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	409 })
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	410
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	411 if annotation["introns"]:
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	412
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	413 s += """
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	414 ann_list[['introns']] = data.table(
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	415 tx = rep(c(%(tx_introns)s), c(%(n_introns)s)),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	416 start = c(%(intron_start)s),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	417 end = c(%(intron_end)s),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	418 strand = c(%(strand)s)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	419 )
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	420 # Create data table for strand arrows
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	421 txarrows = data.table()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	422 introns = ann_list[['introns']]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	423 # Add right-pointing arrows for plus strand
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	424 if ("+" %%in%% introns$strand) {
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	425 txarrows = rbind(
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	426 txarrows,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	427 introns[strand=="+" & end-start>5, list(
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	428 seq(start+4,end,by=%(arrow_space)s)-1,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	429 seq(start+4,end,by=%(arrow_space)s)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	430 ), by=.(tx,start,end)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	431 ]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	432 )
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	433 }
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	434 # Add left-pointing arrows for minus strand
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	435 if ("-" %%in%% introns$strand) {
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	436 txarrows = rbind(txarrows,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	437 introns[strand=="-" & end-start>5,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	438 list(seq(start,max(start+1, end-4),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	439 by=%(arrow_space)s),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	440 seq(start,max(start+1, end-4),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	441 by=%(arrow_space)s)-1
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	442 ),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	443 by=.(tx,start,end)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	444 ]
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	445 )
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	446 }
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	447 """ % ({
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	448 "tx_introns": ",".join(annotation["introns"].keys()),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	449 "n_introns": ",".join(map(str, map(len,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	450 annotation["introns"].values()))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	451 "intron_start": ",".join(map(str, (v[0] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	452 annotation["introns"].values() for v in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	453 vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	454 "intron_end": ",".join(map(str, (v[1] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	455 annotation["introns"].values() for v in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	456 vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	457 "strand": ",".join(map(str, (v[2] for vs in
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	458 annotation["introns"].values() for v in vs))),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	459 "arrow_space": arrow_space,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	460 })
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	461
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	462 s += """
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	463
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	464 gtfp = ggplot()
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	465 if (length(ann_list[['introns']]) > 0) {
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	466 gtfp = gtfp + geom_segment(data = ann_list[['introns']],
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	467 aes(x = start,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	468 xend = end,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	469 y = tx,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	470 yend = tx),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	471 size = 0.3)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	472 gtfp = gtfp + geom_segment(data = txarrows,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	473 aes(x = V1,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	474 xend = V2,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	475 y = tx,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	476 yend = tx),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	477 arrow = arrow(length = unit(0.02, "npc")))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	478 }
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	479 if (length(ann_list[['exons']]) > 0) {
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	480 gtfp = gtfp + geom_segment(data = ann_list[['exons']],
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	481 aes(x = start,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	482 xend = end,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	483 y = tx,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	484 yend = tx),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	485 size = 5,
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	486 alpha = 1)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	487 }
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	488 gtfp = gtfp + scale_y_discrete(expand = c(0, 0.5))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	489 gtfp = gtfp + scale_x_continuous(expand = c(0, 0.25),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	490 limits = c( %s,% s))
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	491 gtfp = gtfp + labs(y = NULL)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	492 gtfp = gtfp + theme(axis.line = element_blank(),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	493 axis.text.x = element_blank(),
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	494 axis.ticks = element_blank())
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	495 """ % (start, end)
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	496
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	497 return s
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	498
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	499
9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc" artbio parents: diff changeset	500 def setup_R_script(h, w, b, label_dict):

0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1 #!/usr/bin/env python

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

2

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

3 # Import modules

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

4 import copy

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

5 import os

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

6 import re

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

7 import subprocess as sp

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

8 import sys

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

9 from argparse import ArgumentParser

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

10 from collections import OrderedDict

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

11

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

12

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

13 def define_options():

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

14 # Argument parsing

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

15 parser = ArgumentParser(description="""Create sashimi plot for a given

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

16 genomic region""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

17 parser.add_argument("-b", "--bam", type=str,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

18 help="""

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

19 Individual bam file or file with a list of bam files.

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

20 In the case of a list of files the format is tsv:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

21 1col: id for bam file,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

22 2col: path of bam file,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

23 3+col: additional columns

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

24 """)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

25 parser.add_argument("-c", "--coordinates", type=str,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

26 help="Genomic region. Format: chr:start-end (1-based)")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

27 parser.add_argument("-o", "--out-prefix", type=str, dest="out_prefix",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

28 default="sashimi",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

29 help="Prefix for plot file name [default=%(default)s]")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

30 parser.add_argument("-S", "--out-strand", type=str, dest="out_strand",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

31 default="both", help="""Only for --strand other than

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

32 'NONE'. Choose which signal strand to plot:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

33 <both> <plus> <minus> [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

34 parser.add_argument("-M", "--min-coverage", type=int, default=1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

35 dest="min_coverage", help="""Minimum number of reads

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

36 supporting a junction to be drawn [default=1]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

37 parser.add_argument("-j", "--junctions-bed", type=str, default="",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

38 dest="junctions_bed", help="""Junction BED file name

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

39 [default=no junction file]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

40 parser.add_argument("-g", "--gtf",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

41 help="Gtf file with annotation (only exons is enough)")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

42 parser.add_argument("-s", "--strand", default="NONE", type=str,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

43 help="""Strand specificity: <NONE> <SENSE> <ANTISENSE>

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

44 <MATE1_SENSE> <MATE2_SENSE> [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

45 parser.add_argument("--shrink", action="store_true",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

46 help="""Shrink the junctions by a factor for nicer

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

47 display [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

48 parser.add_argument("-O", "--overlay", type=int,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

49 help="Index of column with overlay levels (1-based)")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

50 parser.add_argument("-A", "--aggr", type=str, default="",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

51 help="""Aggregate function for overlay:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

52 <mean> <median> <mean_j> <median_j>.

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

53 Use mean_j | median_j to keep density overlay but

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

54 aggregate junction counts [default=no aggregation]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

55 parser.add_argument("-C", "--color-factor", type=int, dest="color_factor",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

56 help="Index of column with color levels (1-based)")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

57 parser.add_argument("--alpha", type=float, default=0.5,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

58 help="""Transparency level for density histogram

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

59 [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

60 parser.add_argument("-P", "--palette", type=str,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

61 help="""Color palette file. tsv file with >=1 columns,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

62 where the color is the first column""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

63 parser.add_argument("-L", "--labels", type=int, dest="labels", default=1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

64 help="""Index of column with labels (1-based)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

65 [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

66 parser.add_argument("--height", type=float, default=2,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

67 help="""Height of the individual signal plot in inches

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

68 [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

69 parser.add_argument("--ann-height", type=float, default=1.5,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

70 dest="ann_height", help="""Height of annotation plot in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

71 inches [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

72 parser.add_argument("--width", type=float, default=10,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

73 help="""Width of the plot in inches

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

74 [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

75 parser.add_argument("--base-size", type=float, default=14,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

76 dest="base_size", help="""Base font size of the plot in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

77 pch [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

78 parser.add_argument("-F", "--out-format", type=str, default="pdf",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

79 dest="out_format", help="""Output file format:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

80 <pdf> <svg> <png> <jpeg> <tiff>

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

81 [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

82 parser.add_argument("-R", "--out-resolution", type=int, default=300,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

83 dest="out_resolution", help="""Output file resolution in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

84 PPI (pixels per inch). Applies only to raster output

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

85 formats [default=%(default)s]""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

86 return parser

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

87

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

88

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

89 def parse_coordinates(c):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

90 c = c.replace(",", "")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

91 chr = c.split(":")[0]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

92 start, end = c.split(":")[1].split("-")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

93 # Convert to 0-based

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

94 start, end = int(start) - 1, int(end)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

95 return chr, start, end

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

96

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

97

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

98 def count_operator(CIGAR_op, CIGAR_len, pos, start, end, a, junctions):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

99

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

100 # Match

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

101 if CIGAR_op == "M":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

102 for i in range(pos, pos + CIGAR_len):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

103 if i < start or i >= end:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

104 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

105 ind = i - start

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

106 a[ind] += 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

107

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

108 # Insertion or Soft-clip

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

109 if CIGAR_op == "I" or CIGAR_op == "S":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

110 return pos

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

111

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

112 # Deletion

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

113 if CIGAR_op == "D":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

114 pass

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

115

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

116 # Junction

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

117 if CIGAR_op == "N":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

118 don = pos

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

119 acc = pos + CIGAR_len

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

120 if don > start and acc < end:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

121 junctions[(don, acc)] = junctions.setdefault((don, acc), 0) + 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

122

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

123 pos = pos + CIGAR_len

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

124

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

125 return pos

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

126

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

127

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

128 def flip_read(s, samflag):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

129 if s == "NONE" or s == "SENSE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

130 return 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

131 if s == "ANTISENSE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

132 return 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

133 if s == "MATE1_SENSE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

134 if int(samflag) & 64:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

135 return 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

136 if int(samflag) & 128:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

137 return 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

138 if s == "MATE2_SENSE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

139 if int(samflag) & 64:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

140 return 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

141 if int(samflag) & 128:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

142 return 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

143

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

144

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

145 def read_bam(f, c, s):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

146

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

147 _, start, end = parse_coordinates(c)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

148

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

149 # Initialize coverage array and junction dict

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

150 a = {"+": [0] * (end - start)}

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

151 junctions = {"+": OrderedDict()}

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

152 if s != "NONE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

153 a["-"] = [0] * (end - start)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

154 junctions["-"] = OrderedDict()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

155

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

156 p = sp.Popen("samtools view %s %s " % (f, c), shell=True, stdout=sp.PIPE)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

157 for line in p.communicate()[0].decode('utf8').strip().split("\n"):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

158

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

159 if line == "":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

160 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

161

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

162 line_sp = line.strip().split("\t")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

163 samflag, read_start, CIGAR = line_sp[1], int(line_sp[3]), line_sp[5]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

164

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

165 # Ignore reads with more exotic CIGAR operators

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

166 if any(map(lambda x: x in CIGAR, ["H", "P", "X", "="])):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

167 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

168

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

169 read_strand = ["+", "-"][flip_read(s, samflag) ^ bool(int(samflag) &

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

170 16)]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

171 if s == "NONE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

172 read_strand = "+"

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

173

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

174 CIGAR_lens = re.split("[MIDNS]", CIGAR)[:-1]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

175 CIGAR_ops = re.split("[0-9]+", CIGAR)[1:]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

176

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

177 pos = read_start

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

178

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

179 for n, CIGAR_op in enumerate(CIGAR_ops):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

180 CIGAR_len = int(CIGAR_lens[n])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

181 pos = count_operator(CIGAR_op, CIGAR_len, pos, start, end,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

182 a[read_strand], junctions[read_strand])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

183

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

184 p.stdout.close()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

185 return a, junctions

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

186

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

187

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

188 def get_bam_path(index, path):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

189 if os.path.isabs(path):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

190 return path

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

191 base_dir = os.path.dirname(index)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

192 return os.path.join(base_dir, path)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

193

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

194

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

195 def read_bam_input(f, overlay, color, label):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

196 if f.endswith(".bam"):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

197 bn = f.strip().split("/")[-1].strip(".bam")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

198 yield bn, f, None, None, bn

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

199 return

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

200 with open(f) as openf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

201 for line in openf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

202 line_sp = line.strip().split("\t")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

203 bam = get_bam_path(f, line_sp[1])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

204 overlay_level = line_sp[overlay-1] if overlay else None

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

205 color_level = line_sp[color-1] if color else None

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

206 label_text = line_sp[label-1] if label else None

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

207 yield line_sp[0], bam, overlay_level, color_level, label_text

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

208

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

209

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

210 def prepare_for_R(a, junctions, c, m):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

211

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

212 _, start, _ = parse_coordinates(args.coordinates)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

213

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

214 # Convert the array index to genomic coordinates

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

215 x = list(i+start for i in range(len(a)))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

216 y = a

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

217

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

218 # Arrays for R

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

219 dons, accs, yd, ya, counts = [], [], [], [], []

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

220

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

221 # Prepare arrays for junctions (which will be the arcs)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

222 for (don, acc), n in junctions.items():

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

223

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

224 # Do not add junctions with less than defined coverage

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

225 if n < m:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

226 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

227

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

228 dons.append(don)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

229 accs.append(acc)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

230 counts.append(n)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

231

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

232 yd.append(a[don - start - 1])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

233 ya.append(a[acc - start + 1])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

234

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

235 return x, y, dons, accs, yd, ya, counts

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

236

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

237

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

238 def intersect_introns(data):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

239 data = sorted(data)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

240 it = iter(data)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

241 a, b = next(it)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

242 for c, d in it:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

243 if b > c:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

244 # Use `if b > c` if you want (1,2), (2,3) not to be

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

245 # treated as intersection.

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

246 b = min(b, d)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

247 a = max(a, c)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

248 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

249 yield a, b

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

250 a, b = c, d

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

251 yield a, b

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

252

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

253

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

254 def shrink_density(x, y, introns):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

255 new_x, new_y = [], []

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

256 shift = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

257 start = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

258 # introns are already sorted by coordinates

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

259 for a, b in introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

260 end = x.index(a)+1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

261 new_x += [int(i-shift) for i in x[start:end]]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

262 new_y += y[start:end]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

263 start = x.index(b)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

264 L = (b-a)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

265 shift += L-L**0.7

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

266 new_x += [int(i-shift) for i in x[start:]]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

267 new_y += y[start:]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

268 return new_x, new_y

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

269

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

270

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

271 def shrink_junctions(dons, accs, introns):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

272 new_dons, new_accs = [0]*len(dons), [0]*len(accs)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

273 shift_acc = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

274 shift_don = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

275 s = set()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

276 junctions = list(zip(dons, accs))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

277 for a, b in introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

278 L = b - a

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

279 shift_acc += L-int(L**0.7)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

280 for i, (don, acc) in enumerate(junctions):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

281 if a >= don and b <= acc:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

282 if (don, acc) not in s:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

283 new_dons[i] = don - shift_don

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

284 new_accs[i] = acc - shift_acc

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

285 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

286 new_accs[i] = acc - shift_acc

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

287 s.add((don, acc))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

288 shift_don = shift_acc

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

289 return new_dons, new_accs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

290

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

291

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

292 def read_palette(f):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

293 palette = "#ff0000", "#00ff00", "#0000ff", "#000000"

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

294 if f:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

295 with open(f) as openf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

296 palette = list(line.split("\t")[0].strip() for line in openf)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

297 return palette

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

298

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

299

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

300 def read_gtf(f, c):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

301 exons = OrderedDict()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

302 transcripts = OrderedDict()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

303 chr, start, end = parse_coordinates(c)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

304 end = end - 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

305 with open(f) as openf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

306 for line in openf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

307 if line.startswith("#"):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

308 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

309 (el_chr, _, el, el_start, el_end, _,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

310 strand, _, tags) = line.strip().split("\t")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

311 if el_chr != chr:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

312 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

313 d = dict(kv.strip().split(" ") for kv in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

314 tags.strip(";").split("; "))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

315 transcript_id = d["transcript_id"]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

316 el_start, el_end = int(el_start) - 1, int(el_end)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

317 strand = '"' + strand + '"'

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

318 if el == "transcript":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

319 if (el_end > start and el_start < end):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

320 transcripts[transcript_id] = (max(start, el_start),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

321 min(end, el_end),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

322 strand)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

323 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

324 if el == "exon":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

325 if (start < el_start < end or start < el_end < end):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

326 exons.setdefault(transcript_id,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

327 []).append((max(el_start, start),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

328 min(end, el_end), strand))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

329

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

330 return transcripts, exons

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

331

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

332

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

333 def make_introns(transcripts, exons, intersected_introns=None):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

334 new_transcripts = copy.deepcopy(transcripts)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

335 new_exons = copy.deepcopy(exons)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

336 introns = OrderedDict()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

337 if intersected_introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

338 for tx, (tx_start, tx_end, strand) in new_transcripts.items():

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

339 total_shift = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

340 for a, b in intersected_introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

341 L = b - a

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

342 shift = L - int(L**0.7)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

343 total_shift += shift

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

344 for i, (exon_start, exon_end, strand) in \

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

345 enumerate(exons.get(tx, [])):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

346 new_exon_start, new_exon_end = new_exons[tx][i][:2]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

347 if a < exon_start:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

348 if b > exon_end:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

349 if i == len(exons[tx])-1:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

350 total_shift = total_shift - shift + \

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

351 (exon_start - a)*(1-int(L**-0.3))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

352 shift = (exon_start - a)*(1-int(L**-0.3))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

353 new_exon_end = new_exons[tx][i][1] - shift

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

354 new_exon_start = new_exons[tx][i][0] - shift

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

355 if b <= exon_end:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

356 new_exon_end = new_exons[tx][i][1] - shift

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

357 new_exons[tx][i] = (new_exon_start, new_exon_end, strand)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

358 tx_start = min(tx_start,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

359 sorted(new_exons.get(tx, [[sys.maxsize]]))[0][0])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

360 new_transcripts[tx] = (tx_start, tx_end - total_shift, strand)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

361

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

362 for tx, (tx_start, tx_end, strand) in new_transcripts.items():

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

363 intron_start = tx_start

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

364 ex_end = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

365 for ex_start, ex_end, strand in sorted(new_exons.get(tx, [])):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

366 intron_end = ex_start

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

367 if tx_start < ex_start:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

368 introns.setdefault(tx, []).append((intron_start, intron_end,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

369 strand))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

370 intron_start = ex_end

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

371 if tx_end > ex_end:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

372 introns.setdefault(tx, []).append((intron_start, tx_end, strand))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

373 d = {'transcripts': new_transcripts,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

374 'exons': new_exons,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

375 'introns': introns}

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

376 return d

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

377

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

378

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

379 def gtf_for_ggplot(annotation, start, end, arrow_bins):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

380 arrow_space = int((end - start)/arrow_bins)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

381 s = """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

382

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

383 # data table with exons

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

384 ann_list = list(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

385 "exons" = data.table(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

386 "introns" = data.table()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

387 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

388 """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

389

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

390 if annotation["exons"]:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

391

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

392 s += """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

393 ann_list[['exons']] = data.table(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

394 tx = rep(c(%(tx_exons)s), c(%(n_exons)s)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

395 start = c(%(exon_start)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

396 end = c(%(exon_end)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

397 strand = c(%(strand)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

398 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

399 """ % ({

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

400 "tx_exons": ",".join(annotation["exons"].keys()),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

401 "n_exons": ",".join(map(str, map(len,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

402 annotation["exons"].values()))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

403 "exon_start": ",".join(map(str, (v[0] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

404 annotation["exons"].values() for v in vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

405 "exon_end": ",".join(map(str, (v[1] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

406 annotation["exons"].values() for v in vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

407 "strand": ",".join(map(str, (v[2] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

408 annotation["exons"].values() for v in vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

409 })

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

410

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

411 if annotation["introns"]:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

412

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

413 s += """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

414 ann_list[['introns']] = data.table(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

415 tx = rep(c(%(tx_introns)s), c(%(n_introns)s)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

416 start = c(%(intron_start)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

417 end = c(%(intron_end)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

418 strand = c(%(strand)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

419 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

420 # Create data table for strand arrows

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

421 txarrows = data.table()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

422 introns = ann_list[['introns']]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

423 # Add right-pointing arrows for plus strand

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

424 if ("+" %%in%% introns$strand) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

425 txarrows = rbind(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

426 txarrows,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

427 introns[strand=="+" & end-start>5, list(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

428 seq(start+4,end,by=%(arrow_space)s)-1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

429 seq(start+4,end,by=%(arrow_space)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

430 ), by=.(tx,start,end)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

431 ]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

432 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

433 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

434 # Add left-pointing arrows for minus strand

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

435 if ("-" %%in%% introns$strand) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

436 txarrows = rbind(txarrows,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

437 introns[strand=="-" & end-start>5,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

438 list(seq(start,max(start+1, end-4),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

439 by=%(arrow_space)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

440 seq(start,max(start+1, end-4),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

441 by=%(arrow_space)s)-1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

442 ),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

443 by=.(tx,start,end)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

444 ]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

445 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

446 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

447 """ % ({

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

448 "tx_introns": ",".join(annotation["introns"].keys()),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

449 "n_introns": ",".join(map(str, map(len,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

450 annotation["introns"].values()))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

451 "intron_start": ",".join(map(str, (v[0] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

452 annotation["introns"].values() for v in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

453 vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

454 "intron_end": ",".join(map(str, (v[1] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

455 annotation["introns"].values() for v in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

456 vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

457 "strand": ",".join(map(str, (v[2] for vs in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

458 annotation["introns"].values() for v in vs))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

459 "arrow_space": arrow_space,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

460 })

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

461

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

462 s += """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

463

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

464 gtfp = ggplot()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

465 if (length(ann_list[['introns']]) > 0) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

466 gtfp = gtfp + geom_segment(data = ann_list[['introns']],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

467 aes(x = start,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

468 xend = end,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

469 y = tx,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

470 yend = tx),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

471 size = 0.3)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

472 gtfp = gtfp + geom_segment(data = txarrows,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

473 aes(x = V1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

474 xend = V2,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

475 y = tx,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

476 yend = tx),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

477 arrow = arrow(length = unit(0.02, "npc")))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

478 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

479 if (length(ann_list[['exons']]) > 0) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

480 gtfp = gtfp + geom_segment(data = ann_list[['exons']],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

481 aes(x = start,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

482 xend = end,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

483 y = tx,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

484 yend = tx),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

485 size = 5,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

486 alpha = 1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

487 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

488 gtfp = gtfp + scale_y_discrete(expand = c(0, 0.5))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

489 gtfp = gtfp + scale_x_continuous(expand = c(0, 0.25),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

490 limits = c( %s,% s))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

491 gtfp = gtfp + labs(y = NULL)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

492 gtfp = gtfp + theme(axis.line = element_blank(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

493 axis.text.x = element_blank(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

494 axis.ticks = element_blank())

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

495 """ % (start, end)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

496

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

497 return s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

498

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

499

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

500 def setup_R_script(h, w, b, label_dict):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

501 s = """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

502 library(ggplot2)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

503 library(grid)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

504 library(gridExtra)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

505 library(data.table)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

506 library(gtable)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

507

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

508 scale_lwd = function(r) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

509 lmin = 0.1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

510 lmax = 4

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

511 return( r*(lmax-lmin)+lmin )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

512 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

513

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

514 base_size = %(b)s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

515 height = ( %(h)s + base_size*0.352777778/67 ) * 1.02

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

516 width = %(w)s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

517 theme_set(theme_bw(base_size=base_size))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

518 theme_update(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

519 plot.margin = unit(c(15,15,15,15), "pt"),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

520 panel.grid = element_blank(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

521 panel.border = element_blank(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

522 axis.line = element_line(size=0.5),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

523 axis.title.x = element_blank(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

524 axis.title.y = element_text(angle=0, vjust=0.5)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

525 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

526

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

527 labels = list(%(labels)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

528

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

529 density_list = list()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

530 junction_list = list()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

531

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

532 """ % ({

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

533 'h': h,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

534 'w': w,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

535 'b': b,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

536 'labels': ",".join(('"%s"="%s"' % (id, lab) for id, lab in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

537 label_dict.items())),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

538 })

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

539 return s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

540

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

541

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

542 def median(lst):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

543 quotient, remainder = divmod(len(lst), 2)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

544 if remainder:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

545 return sorted(lst)[quotient]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

546 return sum(sorted(lst)[quotient - 1:quotient + 1]) / 2.

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

547

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

548

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

549 def mean(lst):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

550 return sum(lst)/len(lst)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

551

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

552

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

553 def make_R_lists(id_list, d, overlay_dict, aggr, intersected_introns):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

554 s = ""

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

555 aggr_f = {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

556 "mean": mean,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

557 "median": median,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

558 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

559 id_list = id_list if not overlay_dict else overlay_dict.keys()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

560 # Iterate over ids to get bam signal and junctions

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

561 for k in id_list:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

562 x, y, dons, accs, yd, ya, counts = [], [], [], [], [], [], []

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

563 if not overlay_dict:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

564 x, y, dons, accs, yd, ya, counts = d[k]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

565 if intersected_introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

566 x, y = shrink_density(x, y, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

567 dons, accs = shrink_junctions(dons, accs, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

568 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

569 for id in overlay_dict[k]:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

570 xid, yid, donsid, accsid, ydid, yaid, countsid = d[id]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

571 if intersected_introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

572 xid, yid = shrink_density(xid, yid, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

573 donsid, accsid = shrink_junctions(donsid, accsid,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

574 intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

575 x += xid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

576 y += yid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

577 dons += donsid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

578 accs += accsid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

579 yd += ydid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

580 ya += yaid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

581 counts += countsid

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

582 if aggr and "_j" not in aggr:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

583 x = d[overlay_dict[k][0]][0]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

584 y = list(map(aggr_f[aggr], zip(*(d[id][1] for id in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

585 overlay_dict[k]))))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

586 if intersected_introns:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

587 x, y = shrink_density(x, y, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

588 # dons, accs, yd, ya, counts = [], [], [], [], []

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

589 s += """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

590 density_list[["%(id)s"]] = data.frame(x = c(%(x)s), y = c(%(y)s))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

591 junction_list[["%(id)s"]] = data.frame(x = c(%(dons)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

592 xend=c(%(accs)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

593 y=c(%(yd)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

594 yend=c(%(ya)s),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

595 count=c(%(counts)s))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

596 """ % ({

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

597 "id": k,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

598 'x': ",".join(map(str, x)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

599 'y': ",".join(map(str, y)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

600 'dons': ",".join(map(str, dons)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

601 'accs': ",".join(map(str, accs)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

602 'yd': ",".join(map(str, yd)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

603 'ya': ",".join(map(str, ya)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

604 'counts': ",".join(map(str, counts)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

605 })

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

606 return s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

607

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

608

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

609 def plot(R_script):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

610 p = sp.Popen("R --vanilla --slave", shell=True, stdin=sp.PIPE)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

611 p.communicate(input=R_script.encode())

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

612 p.stdin.close()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

613 p.wait()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

614 return

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

615

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

616

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

617 def colorize(d, p, color_factor):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

618 levels = sorted(set(d.values()))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

619 n = len(levels)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

620 if n > len(p):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

621 p = (p*n)[:n]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

622 if color_factor:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

623 s = "color_list = list(%s)\n" % (",".join('%s="%s"' % (k,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

624 p[levels.index(v)]) for k, v in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

625 d.items()))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

626 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

627 s = "color_list = list(%s)\n" % (",".join('%s="%s"' % (k, "grey") for

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

628 k, v in d.items()))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

629 return s

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

630

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

631

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

632 if __name__ == "__main__":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

633

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

634 strand_dict = {"plus": "+", "minus": "-"}

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

635

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

636 parser = define_options()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

637 if len(sys.argv) == 1:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

638 parser.print_help()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

639 sys.exit(1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

640 args = parser.parse_args()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

641

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

642 if args.aggr and not args.overlay:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

643 print("""ERROR: Cannot apply aggregate function

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

644 if overlay is not selected.""")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

645 exit(1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

646

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

647 palette = read_palette(args.palette)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

648

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

649 (bam_dict, overlay_dict, color_dict,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

650 id_list, label_dict) = ({"+": OrderedDict()}, OrderedDict(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

651 OrderedDict(), [], OrderedDict())

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

652 if args.strand != "NONE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

653 bam_dict["-"] = OrderedDict()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

654 if args.junctions_bed != "":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

655 junctions_list = []

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

656

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

657 for (id, bam, overlay_level,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

658 color_level, label_text) in read_bam_input(args.bam,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

659 args.overlay,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

660 args.color_factor,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

661 args.labels):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

662 if not os.path.isfile(bam):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

663 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

664 id_list.append(id)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

665 label_dict[id] = label_text

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

666 a, junctions = read_bam(bam, args.coordinates, args.strand)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

667 if a.keys() == ["+"] and all(map(lambda x: x == 0,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

668 list(a.values()[0]))):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

669 print("ERROR: No reads in the specified area.")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

670 exit(1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

671 for strand in a:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

672 # Store junction information

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

673 if args.junctions_bed:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

674 for k, v in zip(junctions[strand].keys(),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

675 junctions[strand].values()):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

676 if v > args.min_coverage:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

677 junctions_list.append('\t'.join([args.coordinates.split

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

678 (':')[0], str(k[0]), str(k[1]),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

679 id, str(v), strand]))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

680 bam_dict[strand][id] = prepare_for_R(a[strand],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

681 junctions[strand],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

682 args.coordinates,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

683 args.min_coverage)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

684 if color_level is None:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

685 color_dict.setdefault(id, id)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

686 if overlay_level is not None:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

687 overlay_dict.setdefault(overlay_level, []).append(id)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

688 label_dict[overlay_level] = overlay_level

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

689 color_dict.setdefault(overlay_level, overlay_level)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

690 if overlay_level is None:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

691 color_dict.setdefault(id, color_level)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

692

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

693 # No bam files

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

694 if not bam_dict["+"]:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

695 print("ERROR: No available bam files.")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

696 exit(1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

697

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

698 # Write junctions to BED

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

699 if args.junctions_bed:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

700 if not args.junctions_bed.endswith('.bed'):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

701 args.junctions_bed = args.junctions_bed + '.bed'

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

702 jbed = open(args.junctions_bed, 'w')

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

703 jbed.write('\n'.join(sorted(junctions_list)))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

704 jbed.close()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

705

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

706 if args.gtf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

707 transcripts, exons = read_gtf(args.gtf, args.coordinates)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

708

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

709 if args.out_format not in ('pdf', 'png', 'svg', 'tiff', 'jpeg'):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

710 print("""ERROR: Provided output format '%s' is not available.

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

711 Please select among 'pdf', 'png', 'svg',

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

712 'tiff' or 'jpeg'""" % args.out_format)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

713 exit(1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

714

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

715 # Iterate for plus and minus strand

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

716 for strand in bam_dict:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

717

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

718 # Output file name (allow tiff/tif and jpeg/jpg extensions)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

719 if args.out_prefix.endswith(('.pdf', '.png', '.svg', '.tiff',

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

720 '.tif', '.jpeg', '.jpg')):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

721 out_split = os.path.splitext(args.out_prefix)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

722 if (args.out_format == out_split[1][1:] or

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

723 args.out_format == 'tiff'

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

724 and out_split[1] in ('.tiff', '.tif') or

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

725 args.out_format == 'jpeg'

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

726 and out_split[1] in ('.jpeg', '.jpg')):

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

727 args.out_prefix = out_split[0]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

728 out_suffix = out_split[1][1:]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

729 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

730 out_suffix = args.out_format

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

731 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

732 out_suffix = args.out_format

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

733 out_prefix = args.out_prefix + "_" + strand

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

734 if args.strand == "NONE":

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

735 out_prefix = args.out_prefix

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

736 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

737 if args.out_strand != "both" \

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

738 and strand != strand_dict[args.out_strand]:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

739 continue

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

740

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

741 # Find set of junctions to perform shrink

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

742 intersected_introns = None

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

743 if args.shrink:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

744 introns = (v for vs in bam_dict[strand].values() for v in

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

745 zip(vs[2], vs[3]))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

746 intersected_introns = list(intersect_introns(introns))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

747

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

748 # *** PLOT *** Define plot height

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

749 bam_height = args.height * len(id_list)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

750 if args.overlay:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

751 bam_height = args.height * len(overlay_dict)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

752 if args.gtf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

753 bam_height += args.ann_height

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

754

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

755 # *** PLOT *** Start R script by loading libraries,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

756 # initializing variables, etc...

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

757 R_script = setup_R_script(bam_height, args.width,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

758 args.base_size, label_dict)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

759

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

760 R_script += colorize(color_dict, palette, args.color_factor)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

761

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

762 # *** PLOT *** Prepare annotation plot only for the first bam file

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

763 arrow_bins = 50

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

764 if args.gtf:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

765 # Make introns from annotation (they are shrunk if required)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

766 annotation = make_introns(transcripts, exons, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

767 x = list(bam_dict[strand].values())[0][0]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

768 if args.shrink:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

769 x, _ = shrink_density(x, x, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

770 R_script += gtf_for_ggplot(annotation, x[0], x[-1], arrow_bins)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

771

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

772 R_script += make_R_lists(id_list, bam_dict[strand], overlay_dict,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

773 args.aggr, intersected_introns)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

774

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

775 R_script += """

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

776

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

777 pdf(NULL) # just to remove the blank pdf produced by ggplotGrob

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

778 # fix problems with ggplot2 vs >3.0.0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

779 if(packageVersion('ggplot2') >= '3.0.0'){

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

780 vs = 1

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

781 } else {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

782 vs = 0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

783 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

784

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

785 density_grobs = list();

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

786

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

787 for (bam_index in 1:length(density_list)) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

788

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

789 id = names(density_list)[bam_index]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

790 d = data.table(density_list[[id]])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

791 junctions = data.table(junction_list[[id]])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

792

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

793 maxheight = max(d[['y']])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

794

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

795 # Density plot

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

796 gp = ggplot(d) + geom_bar(aes(x, y), width=1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

797 position='identity',

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

798 stat='identity',

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

799 fill=color_list[[id]],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

800 alpha=%(alpha)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

801 gp = gp + labs(y=labels[[id]])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

802 gp = gp + scale_x_continuous(expand=c(0,0.2))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

803

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

804 # fix problems with ggplot2 vs >3.0.0

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

805 if(packageVersion('ggplot2') >= '3.0.0') {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

806 gp = gp +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

807 scale_y_continuous(breaks =

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

808 ggplot_build(gp

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

809 )$layout$panel_params[[1]]$y.major_source)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

810 } else {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

811 gp = gp +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

812 scale_y_continuous(breaks =

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

813 ggplot_build(gp

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

814 )$layout$panel_ranges[[1]]$y.major_source)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

815 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

816

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

817 # Aggregate junction counts

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

818 row_i = c()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

819 if (nrow(junctions) >0 ) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

820

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

821 junctions$jlabel = as.character(junctions$count)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

822 junctions = setNames(junctions[,.(max(y),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

823 max(yend),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

824 round(mean(count)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

825 paste(jlabel,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

826 collapse=",")),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

827 keyby=.(x,xend)],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

828 names(junctions))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

829 if ("%(args.aggr)s" != "") {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

830 junctions = setNames(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

831 junctions[,.(max(y),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

832 max(yend),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

833 round(%(args.aggr)s(count)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

834 round(%(args.aggr)s(count))),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

835 keyby=.(x,xend)],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

836 names(junctions))

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

837 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

838 # The number of rows (unique junctions per bam) has to be

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

839 # calculated after aggregation

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

840 row_i = 1:nrow(junctions)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

841 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

842

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

843

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

844 for (i in row_i) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

845

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

846 j_tot_counts = sum(junctions[['count']])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

847

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

848 j = as.numeric(junctions[i,1:5])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

849

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

850 if ("%(args.aggr)s" != "") {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

851 j[3] = as.numeric(d[x==j[1]-1,y])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

852 j[4] = as.numeric(d[x==j[2]+1,y])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

853 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

854

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

855 # Find intron midpoint

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

856 xmid = round(mean(j[1:2]), 1)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

857 ymid = max(j[3:4]) * 1.2

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

858

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

859 # Thickness of the arch

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

860 lwd = scale_lwd(j[5]/j_tot_counts)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

861

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

862 curve_par = gpar(lwd=lwd, col=color_list[[id]])

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

863

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

864 # Arc grobs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

865

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

866 # Choose position of the arch (top or bottom)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

867 nss = i

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

868 if (nss%%%%2 == 0) { #bottom

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

869 ymid = -0.3 * maxheight

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

870 # Draw the arcs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

871 # Left

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

872 curve = xsplineGrob(x = c(0, 0, 1, 1),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

873 y = c(1, 0, 0, 0),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

874 shape = 1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

875 gp = curve_par)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

876 gp = gp + annotation_custom(grob = curve,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

877 j[1], xmid, 0, ymid)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

878 # Right

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

879 curve = xsplineGrob(x = c(1, 1, 0, 0),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

880 y = c(1, 0, 0, 0),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

881 shape = 1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

882 gp = curve_par)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

883 gp = gp + annotation_custom(grob = curve,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

884 xmid,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

885 j[2],

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

886 0, ymid)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

887 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

888

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

889 if (nss%%%%2 != 0) { #top

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

890 # Draw the arcs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

891 # Left

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

892 curve = xsplineGrob(x = c(0, 0, 1, 1),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

893 y = c(0, 1, 1, 1),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

894 shape = 1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

895 gp = curve_par)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

896 gp = gp + annotation_custom(grob = curve,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

897 j[1], xmid, j[3], ymid)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

898 # Right

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

899 curve = xsplineGrob(x = c(1, 1, 0, 0),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

900 y = c(0, 1, 1, 1),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

901 shape = 1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

902 gp = curve_par)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

903 gp = gp + annotation_custom(grob = curve,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

904 xmid, j[2], j[4], ymid)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

905 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

906

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

907 # Add junction labels

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

908 gp = gp + annotate("label", x = xmid, y = ymid,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

909 label = as.character(junctions[i,6]),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

910 vjust = 0.5, hjust = 0.5,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

911 label.padding = unit(0.01, "lines"),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

912 label.size = NA,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

913 size = (base_size*0.352777778)*0.6)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

914

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

915 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

916

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

917 gpGrob = ggplotGrob(gp);

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

918 gpGrob$layout$clip[gpGrob$layout$name=="panel"] <- "off"

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

919 if (bam_index == 1) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

920 # fix problems ggplot2 vs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

921 maxWidth = gpGrob$widths[2+vs] + gpGrob$widths[3+vs];

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

922 maxYtextWidth = gpGrob$widths[3+vs];

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

923 # Extract x axis grob (trim=F --> keep empty cells)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

924 xaxisGrob <- gtable_filter(gpGrob, "axis-b", trim=F)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

925 # fix problems ggplot2 vs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

926 xaxisGrob$heights[8+vs] = gpGrob$heights[1]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

927 x.axis.height = gpGrob$heights[7+vs] + gpGrob$heights[1]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

928 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

929

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

930

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

931 # Remove x axis from all density plots

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

932 kept_names = gpGrob$layout$name[gpGrob$layout$name != "axis-b"]

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

933 gpGrob <- gtable_filter(gpGrob,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

934 paste(kept_names, sep = "",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

935 collapse = "|"),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

936 trim=F)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

937

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

938 # Find max width of y text and y label and max width of y text

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

939 # fix problems ggplot2 vs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

940 maxWidth = grid::unit.pmax(maxWidth,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

941 gpGrob$widths[2+vs] +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

942 gpGrob$widths[3+vs]);

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

943 maxYtextWidth = grid::unit.pmax(maxYtextWidth,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

944 gpGrob$widths[3+vs]);

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

945 density_grobs[[id]] = gpGrob;

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

946 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

947

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

948 # Add x axis grob after density grobs BEFORE annotation grob

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

949 density_grobs[["xaxis"]] = xaxisGrob

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

950

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

951 # Annotation grob

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

952 if (%(args.gtf)s == 1) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

953 gtfGrob = ggplotGrob(gtfp);

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

954 maxWidth = grid::unit.pmax(maxWidth,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

955 gtfGrob$widths[2+vs] +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

956 gtfGrob$widths[3+vs]);

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

957 density_grobs[['gtf']] = gtfGrob;

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

958 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

959

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

960 # Reassign grob widths to align the plots

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

961 for (id in names(density_grobs)) {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

962 density_grobs[[id]]$widths[1] <-

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

963 density_grobs[[id]]$widths[1] +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

964 maxWidth - (density_grobs[[id]]$widths[2 + vs] +

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

965 maxYtextWidth)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

966 # fix problems ggplot2 vs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

967 density_grobs[[id]]$widths[3 + vs] <-

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

968 maxYtextWidth # fix problems ggplot2 vs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

969 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

970

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

971 # Heights for density, x axis and annotation

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

972 heights = unit.c(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

973 unit(rep(%(signal_height)s,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

974 length(density_list)), "in"),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

975 x.axis.height,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

976 unit(%(ann_height)s*%(args.gtf)s, "in")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

977 )

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

978

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

979 # Arrange grobs

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

980 argrobs = arrangeGrob(

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

981 grobs=density_grobs,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

982 ncol=1,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

983 heights = heights,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

984 );

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

985

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

986 # Save plot to file in the requested format

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

987 if ("%(out_format)s" == "tiff"){

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

988 # TIFF images will be lzw-compressed

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

989 ggsave("%(out)s",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

990 plot = argrobs,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

991 device = "tiff",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

992 width = width,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

993 height = height,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

994 units = "in",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

995 dpi = %(out_resolution)s,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

996 compression = "lzw")

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

997 } else {

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

998 ggsave("%(out)s",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

999 plot = argrobs,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1000 device = "%(out_format)s",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1001 width = width,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1002 height = height,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1003 units = "in",

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1004 dpi = %(out_resolution)s)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1005 }

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1006

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1007 dev.log = dev.off()

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1008

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1009 """ % ({

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1010 "out": "%s.%s" % (out_prefix, out_suffix),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1011 "out_format": args.out_format,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1012 "out_resolution": args.out_resolution,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1013 "args.gtf": float(bool(args.gtf)),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1014 "args.aggr": args.aggr.rstrip("_j"),

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1015 "signal_height": args.height,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1016 "ann_height": args.ann_height,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1017 "alpha": args.alpha,

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1018 })

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1019 if os.getenv('GGSASHIMI_DEBUG') is not None:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1020 with open("R_script", 'w') as r:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1021 r.write(R_script)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1022 else:

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1023 plot(R_script)

9304dd9a16a2 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot commit 746c03a1187e1d708af8628920a0c615cddcdacc"

artbio

parents:

diff changeset

1024 exit()

Mercurial > repos > artbio > sashimi_plot

annotate sashimi-plot.py @ 0:9304dd9a16a2 draft