Mercurial > repos > mheinzl > fsd_regions

annotate fsd_regions.py @ 14:6879295d3f11 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
author mheinzl
date Tue, 08 Jan 2019 09:50:01 -0500
parents 63432e6f6a61
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
1 #!/usr/bin/env python
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
2
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
3 # Family size distribution of tags which were aligned to the reference genome
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
4 #
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
5 # Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
6 # Contact: monika.heinzl@edumail.at
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
7 #
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
8 # Takes at least one TABULAR file with tags before the alignment to the SSCS,
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
9 # a BAM file with tags of reads that overlap the regions of the reference genome and
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
10 # an optional BED file with chromosome, start and stop position of the regions as input.
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
11 # The program produces a plot which shows the distribution of family sizes of the tags from the input files and
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
12 # a tabular file with the data of the plot.
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
13
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
14 # USAGE: python FSD_regions.py --inputFile filenameSSCS --inputName1 filenameSSCS
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
15 # --bamFile DCSbamFile --rangesFile BEDfile --output_tabular outptufile_name_tabular
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
16 # --output_pdf outputfile_name_pdf
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
17
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
18 import argparse
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
19 import collections
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
20 import re
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
21 import sys
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
22
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
23 import matplotlib.pyplot as plt
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
24 import numpy as np
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
25 import pysam
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
26 from matplotlib.backends.backend_pdf import PdfPages
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
27
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
28 plt.switch_backend('agg')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
29
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
30
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
31 def readFileReferenceFree(file, delim):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
32 with open(file, 'r') as dest_f:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
33 data_array = np.genfromtxt(dest_f, skip_header=0, delimiter=delim, comments='#', dtype='string')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
34 return(data_array)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
35
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
36
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
37 def make_argparser():
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
38 parser = argparse.ArgumentParser(description='Family Size Distribution of tags which were aligned to regions of the reference genome')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
39 parser.add_argument('--inputFile', help='Tabular File with three columns: ab or ba, tag and family size.')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
40 parser.add_argument('--inputName1')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
41 parser.add_argument('--bamFile', help='BAM file with aligned reads.')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
42 parser.add_argument('--rangesFile', default=None, help='BED file with chromosome, start and stop positions.')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
43 parser.add_argument('--output_pdf', default="data.pdf", type=str, help='Name of the pdf and tabular file.')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
44 parser.add_argument('--output_tabular', default="data.tabular", type=str, help='Name of the pdf and tabular file.')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
45 return parser
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
46
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
47
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
48 def compare_read_families_refGenome(argv):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
49 parser = make_argparser()
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
50 args = parser.parse_args(argv[1:])
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
51
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
52 firstFile = args.inputFile
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
53 name1 = args.inputName1
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
54 name1 = name1.split(".tabular")[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
55 bamFile = args.bamFile
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
56
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
57 rangesFile = args.rangesFile
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
58 title_file = args.output_pdf
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
59 title_file2 = args.output_tabular
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
60 sep = "\t"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
61
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
62 with open(title_file2, "w") as output_file, PdfPages(title_file) as pdf:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
63 data_array = readFileReferenceFree(firstFile, "\t")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
64 pysam.index(bamFile)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
65
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
66 bam = pysam.AlignmentFile(bamFile, "rb")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
67 qname_dict = collections.OrderedDict()
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
68
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
69 if rangesFile != str(None):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
70 with open(rangesFile, 'r') as regs:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
71 range_array = np.genfromtxt(regs, skip_header=0, delimiter='\t', comments='#', dtype='string')
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
72
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
73 if range_array.ndim == 0:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
74 print("Error: file has 0 lines")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
75 exit(2)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
76
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
77 if range_array.ndim == 1:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
78 chrList = range_array[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
79 start_posList = range_array[1].astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
80 stop_posList = range_array[2].astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
81 chrList = [chrList.tolist()]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
82 start_posList = [start_posList.tolist()]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
83 stop_posList = [stop_posList.tolist()]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
84 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
85 chrList = range_array[:, 0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
86 start_posList = range_array[:, 1].astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
87 stop_posList = range_array[:, 2].astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
88
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
89 if len(start_posList) != len(stop_posList):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
90 print("start_positions and end_positions do not have the same length")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
91 exit(3)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
92
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
93 chrList = np.array(chrList)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
94 start_posList = np.array(start_posList).astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
95 stop_posList = np.array(stop_posList).astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
96 for chr, start_pos, stop_pos in zip(chrList, start_posList, stop_posList):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
97 chr_start_stop = "{}_{}_{}".format(chr, start_pos, stop_pos)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
98 qname_dict[chr_start_stop] = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
99 for read in bam.fetch(chr.tobytes(), start_pos, stop_pos):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
100 if not read.is_unmapped:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
101 if re.search('_', read.query_name):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
102 tags = re.split('_', read.query_name)[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
103 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
104 tags = read.query_name
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
105 qname_dict[chr_start_stop].append(tags)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
106
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
107 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
108 for read in bam.fetch():
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
109 if not read.is_unmapped:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
110 if re.search(r'_', read.query_name):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
111 tags = re.split('_', read.query_name)[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
112 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
113 tags = read.query_name
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
114
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
115 if read.reference_name not in qname_dict.keys():
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
116 qname_dict[read.reference_name] = [tags]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
117 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
118 qname_dict[read.reference_name].append(tags)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
119
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
120 seq = np.array(data_array[:, 1])
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
121 tags = np.array(data_array[:, 2])
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
122 quant = np.array(data_array[:, 0]).astype(int)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
123 group = np.array(qname_dict.keys())
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
124
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
125 all_ab = seq[np.where(tags == "ab")[0]]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
126 all_ba = seq[np.where(tags == "ba")[0]]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
127 quant_ab = quant[np.where(tags == "ab")[0]]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
128 quant_ba = quant[np.where(tags == "ba")[0]]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
129
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
130 seqDic_ab = dict(zip(all_ab, quant_ab))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
131 seqDic_ba = dict(zip(all_ba, quant_ba))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
132
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
133 lst_ab = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
134 lst_ba = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
135 quantAfterRegion = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
136 for i in group:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
137 lst_ab_r = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
138 lst_ba_r = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
139 seq_mut = qname_dict[i]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
140 if rangesFile == str(None):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
141 seq_mut, seqMut_index = np.unique(np.array(seq_mut), return_index=True)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
142 for r in seq_mut:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
143 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
144 splitted_tag = re.split('\.', r)[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
145 direction = re.split('\.', r)[1]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
146
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
147 if direction == "ab":
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
148 count_ab = seqDic_ab.get(splitted_tag)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
149 lst_ab_r.append(count_ab)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
150 lst_ab.append(count_ab)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
151
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
152 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
153 count_ba = seqDic_ba.get(splitted_tag)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
154 lst_ba_r.append(count_ba)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
155 lst_ba.append(count_ba)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
156 else: # BAM file with DCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
157 count_ab = seqDic_ab.get(r)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
158 lst_ab_r.append(count_ab)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
159 lst_ab.append(count_ab)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
160 count_ba = seqDic_ba.get(r)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
161 lst_ba_r.append(count_ba)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
162 lst_ba.append(count_ba)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
163
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
164 dataAB = np.array(lst_ab_r)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
165 dataBA = np.array(lst_ba_r)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
166 bigFamilies = np.where(dataAB > 20)[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
167 dataAB[bigFamilies] = 22
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
168 bigFamilies = np.where(dataBA > 20)[0]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
169 dataBA[bigFamilies] = 22
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
170
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
171 quantAll = np.concatenate((dataAB, dataBA))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
172 quantAfterRegion.append(quantAll)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
173
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
174 quant_ab = np.array(lst_ab)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
175 quant_ba = np.array(lst_ba)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
176 length_regions = len(np.concatenate(quantAfterRegion))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
177
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
178 maximumX = np.amax(np.concatenate(quantAfterRegion))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
179 minimumX = np.amin(np.concatenate(quantAfterRegion))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
180
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
181 # PLOT
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
182 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
183 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
184 plt.rcParams['xtick.labelsize'] = 14
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
185 plt.rcParams['ytick.labelsize'] = 14
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
186 plt.rcParams['patch.edgecolor'] = "black"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
187 fig = plt.figure()
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
188 plt.subplots_adjust(bottom=0.3)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
189
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
190 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"]
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
191
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
192 col = []
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
193 for i in range(0, len(group)):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
194 col.append(colors[i])
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
195
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
196 counts = plt.hist(quantAfterRegion, bins=range(minimumX, maximumX + 1), stacked=False, label=group,
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
197 align="left", alpha=1, color=col, edgecolor="black", linewidth=1)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
198 ticks = np.arange(minimumX - 1, maximumX, 1)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
199
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
200 ticks1 = map(str, ticks)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
201 ticks1[len(ticks1) - 1] = ">20"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
202 plt.xticks(np.array(ticks), ticks1)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
203 count = np.bincount(map(int, quant_ab)) # original counts
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
204
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
205 legend = "max. family size:\nabsolute frequency:" \
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
206 "\nrelative frequency:\n\ntotal nr. of reads:\n(before SSCS building)"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
207 plt.text(0.15, 0.085, legend, size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
208
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
209 legend = "AB\n{}\n{}\n{:.5f}\n\n{:,}".format(max(map(int, quant_ab)), count[len(count) - 1], float(count[len(count) - 1]) / sum(count), sum(np.array(data_array[:, 0]).astype(int)))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
210 plt.text(0.35, 0.105, legend, size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
211
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
212 count2 = np.bincount(map(int, quant_ba)) # original counts
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
213
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
214 legend = "BA\n{}\n{}\n{:.5f}" \
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
215 .format(max(map(int, quant_ba)), count2[len(count2) - 1], float(count2[len(count2) - 1]) / sum(count2))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
216 plt.text(0.45, 0.1475, legend, size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
217
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
218 plt.text(0.53, 0.2125, "total nr. of tags:", size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
219 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
220 plt.text(0.85, 0.2125, "{:,}".format(length_regions), size=11,
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
221 transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
222 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
223 plt.text(0.85, 0.2125, "{:,} ({:,})".format(length_regions, length_regions / 2), size=11,
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
224 transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
225 legend4 = "* In the plot, both family sizes of the ab and ba strands were used." \
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
226 "\nWhereas the total numbers indicate only the single count of the tags per region.\n"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
227 plt.text(0.1, 0.01, legend4, size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
228
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
229 space = 0
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
230 for i, count in zip(group, quantAfterRegion):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
231 plt.text(0.53, 0.15 - space, "{}:\n".format(i), size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
232 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
233 plt.text(0.85, 0.15 - space, "{:,}\n".format(len(count)), size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
234 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
235 plt.text(0.85, 0.15 - space, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
236 space = space + 0.02
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
237
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
238 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
239 plt.xlabel("Family size", fontsize=14)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
240 plt.ylabel("Absolute Frequency", fontsize=14)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
241 plt.grid(b=True, which="major", color="#424242", linestyle=":")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
242 plt.margins(0.01, None)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
243
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
244 pdf.savefig(fig, bbox_inch="tight")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
245 plt.close()
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
246
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
247 output_file.write("Dataset:{}{}\n".format(sep, name1))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
248 output_file.write("{}AB{}BA\n".format(sep, sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
249 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba))))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
250 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
251 output_file.write("relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep, float(count2[len(count2) - 1]) / sum(count2)))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
252 output_file.write("total nr. of reads{}{}\n".format(sep, sum(np.array(data_array[:, 0]).astype(int))))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
253 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
254 output_file.write("total nr. of tags{}{}\n".format(sep, length_regions))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
255 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
256 output_file.write("total nr. of tags{}{} ({})\n".format(sep, length_regions, length_regions / 2))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
257 output_file.write("\n\nValues from family size distribution\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
258 output_file.write("{}".format(sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
259 for i in group:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
260 output_file.write("{}{}".format(i, sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
261 output_file.write("\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
262
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
263 j = 0
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
264 for fs in counts[1][0:len(counts[1]) - 1]:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
265 if fs == 21:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
266 fs = ">20"
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
267 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
268 fs = "={}".format(fs)
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
269 output_file.write("FS{}{}".format(fs, sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
270 if len(group) == 1:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
271 output_file.write("{}{}".format(int(counts[0][j]), sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
272 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
273 for n in range(len(group)):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
274 output_file.write("{}{}".format(int(counts[0][n][j]), sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
275 output_file.write("\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
276 j += 1
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
277 output_file.write("sum{}".format(sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
278
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
279 if len(group) == 1:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
280 output_file.write("{}{}".format(int(sum(counts[0])), sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
281 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
282 for i in counts[0]:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
283 output_file.write("{}{}".format(int(sum(i)), sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
284 output_file.write("\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
285 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
286 output_file.write("\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
287 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
288 output_file.write("\n\nIn the plot, both family sizes of the ab and ba strands were used."
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
289 "\nWhereas the total numbers indicate only the single count of the tags per region.\n")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
290 output_file.write("Region{}total nr. of tags per region\n".format(sep))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
291 for i, count in zip(group, quantAfterRegion):
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
292 if re.search('\.', r): # BAM file with SSCS tags
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
293 output_file.write("{}{}{}\n".format(i, sep, len(count)))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
294 else:
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
295 output_file.write("{}{}{}\n".format(i, sep, len(count) / 2))
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
296
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
297 print("Files successfully created!")
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
298
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
299
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
300 if __name__ == '__main__':
6879295d3f11 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 13
diff changeset
301 sys.exit(compare_read_families_refGenome(sys.argv))