dewseq: dewseq_wrapper.py annotate

annotate dewseq_wrapper.py @ 0:e1cb2e012307 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"

author	rnateam
date	Thu, 20 Oct 2022 08:18:30 +0000
parents
children

rev	line source
0 e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	1 #!/usr/bin/env python3
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	2
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	3 import argparse
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	4 import os
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	5 import re
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	6 import shutil
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	7 import subprocess
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	8
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	9
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	10 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	11 DEWSeq wrapper script dependencies:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	12 conda install -c bioconda bioconductor-dewseq
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	13 conda install -c conda-forge r-rmarkdown
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	14 conda install -c bioconda bioconductor-biocstyle
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	15 conda install -c conda-forge r-tidyverse
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	16 conda install -c bioconda r-ggrepel
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	17 conda install -c bioconda bioconductor-ihw
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	18
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	19 Wrapper for DEWSeq R markdown file:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	20 https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers/tree/master/Parametrized_Rmd
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	21
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	22
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	23 Test runs
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	24 =========
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	25
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	26 # This reports 150 significant regions.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	27 python dewseq_wrapper.py --annot test-data/windows.exp.txt --matrix test-data/Rbp_count_matrix.exp.txt --info test-data/sample_info.exp.txt --out test_out --ds-pvc 0.5
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	28
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	29 # Wherease, with LRT, DEWSeq reports just one siginificant region.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	30 python dewseq_wrapper.py --annot test-data/windows.exp.txt --matrix test-data/Rbp_count_matrix.exp.txt --info test-data/sample_info.exp.txt --out test2_out --ds-pvc 0.5 --ds-use-lrt
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	31
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	32 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	33
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	34 ################################################################################
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	35
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	36
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	37 def setup_argument_parser():
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	38 """Setup argparse parser."""
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	39 help_description = """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	40 Wrapping DEWSeq R markdown script, to call peak regions on the CLIP-seq data,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	41 preprocessed by htseq-clip.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	42 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	43 # Define argument parser.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	44 p = argparse.ArgumentParser(add_help=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	45 prog="dewseq_wrapper.py",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	46 description=help_description,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	47 formatter_class=argparse.MetavarTypeHelpFormatter)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	48
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	49 # Required arguments.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	50 p.add_argument("-h", "--help",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	51 action="help",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	52 help="Print help message")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	53 p.add_argument("--annot",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	54 dest="in_annot",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	55 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	56 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	57 required=True,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	58 help="DEWseq annotation file, i.e. windows mapped to IDs table file (output of htseq-clip mapToId)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	59 p.add_argument("--matrix",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	60 dest="in_matrix",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	61 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	62 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	63 required=True,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	64 help="DEWseq count matrix file (output of htseq-clip createMatrix)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	65 p.add_argument("--info",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	66 dest="in_info",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	67 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	68 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	69 required=True,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	70 help="DEWseq sample information file (output of htsc_create_count_table.py / htseq-clip Create count table Galaxy wrapper)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	71 p.add_argument("--out",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	72 dest="out_folder",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	73 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	74 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	75 required=True,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	76 help="Results output folder")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	77 p.add_argument("--ds-ms",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	78 dest="ds_ms",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	79 type=int,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	80 metavar='int',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	81 default=2,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	82 help="DEWSeq min_sample parameter. Keep only the windows with at least min_sample number of samples with crosslink site count > min_count (default: 2)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	83 p.add_argument("--ds-mc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	84 dest="ds_mc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	85 type=int,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	86 metavar='int',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	87 default=2,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	88 help="DEWSeq min_count parameter. Minimum crosslink site per window per sample (default: 2)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	89 p.add_argument("--ds-pvc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	90 dest="ds_pvc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	91 type=float,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	92 metavar='float',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	93 default=0.1,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	94 help="DEWSeq p_value_cutoff parameter. p adjusted value threshold for significant windows (default: 0.1)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	95 p.add_argument("--ds-lfcc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	96 dest="ds_lfcc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	97 type=float,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	98 metavar='float',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	99 default=1,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	100 help="DEWSeq lfc_cutoff parameter. Log2 fold change threshold for significant windows (default: 1)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	101 p.add_argument("--ds-oc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	102 dest="ds_use_oc",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	103 default=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	104 action="store_true",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	105 help="DEWSeq overlap_correction parameter. By default FALSE, i.e., do not adjust p-value for overlapping windows. If TRUE use Bonferroni family wise error rate correction on overlapping sliding windows (default: false)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	106 p.add_argument("--ds--disable-ihw",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	107 dest="ds_disable_ihw",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	108 default=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	109 action="store_true",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	110 help="Disable DEWSeq IHW parameter. By default, use IHW for multiple tesing correction instead of default BH (Benjamini Hochberg). NOTE: We recommend using IHW instead of default BH for FDR correction")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	111 p.add_argument("--ds--disable-df",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	112 dest="ds_disable_df",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	113 default=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	114 action="store_true",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	115 help="Disable DEWSeq decide_fit parameter. By default, decide on dispersion estimation fit type local or parametric. If disabled, Use parametric fit. NOTE: decide_fit=TRUE will fit data using both parametric and local fit types and will choose the best fit of the two (see DESeq2 vignette for details). Typically, this should give better results compared to using the default fit type parametric. But, keep in mind that this will also increase the total run time")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	116 p.add_argument("--ds-use-lrt",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	117 dest="ds_use_lrt",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	118 default=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	119 action="store_true",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	120 help="DEWSeq LRT parameter. Use LRT if the given value is TRUE (see DESeq2 vignette for details). By default, DEWSeq uses Wald test. NOTE: In our experience, LRT is more accurate than Wald test. But, keep in mind that LRT is a stringent test in comparison to Wald. So if your protein of interest is a very active binder, run the analysis with LRT=TRUE, otherwise use it with caution as you may end up with no significant windows or regions in your final output")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	121 p.add_argument("--ds-id",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	122 dest="ds_id",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	123 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	124 default="RBP",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	125 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	126 help="DEWSeq dataset ID for output report (default: RBP)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	127 p.add_argument("--ds-markdown",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	128 dest="ds_markdown",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	129 type=str,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	130 default="analyseStudy.Rmd",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	131 metavar='str',
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	132 help="Provide path to DEWSeq R markdown file. By default assumed to be in working directory")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	133 p.add_argument("--copy-md",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	134 dest="copy_markdown",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	135 default=False,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	136 action="store_true",
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	137 help="Copy DEWSeq R markdown file to output directory and execute [sic!] it there (default: False)")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	138 return p
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	139
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	140
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	141 ################################################################################
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	142
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	143 def count_file_rows(in_file,
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	144 nr_cols=False):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	145 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	146 Count number of file rows. If nr_cols set, demand certain (nr_cols) number
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	147 of columns (separated by tab), in order for row to be counted.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	148
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	149 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	150 c = 0
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	151 with open(in_file) as f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	152 for line in f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	153 cols = line.strip().split("\t")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	154 if nr_cols:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	155 if len(cols) == nr_cols:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	156 c += 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	157 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	158 c += 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	159 f.closed
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	160 return c
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	161
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	162
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	163 ################################################################################
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	164
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	165 def check_two_dic_same_keys(d1, d2):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	166 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	167 Check if two dictionaries have same keys.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	168
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	169 >>> d1 = {'k1': 1, 'k2': 2}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	170 >>> d2 = {'k1': 3, 'k2': 4}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	171 >>> check_two_dic_same_keys(d1, d2)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	172 True
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	173 >>> d2 = {'k1': 3, 'k3': 4}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	174 >>> check_two_dic_same_keys(d1, d2)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	175 False
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	176
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	177 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	178 assert d1, "given dictionary d1 empty"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	179 assert d2, "given dictionary d2 empty"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	180 for k in d1:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	181 if k not in d2:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	182 return False
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	183 for k in d2:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	184 if k not in d1:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	185 return False
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	186 return True
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	187
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	188
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	189 ################################################################################
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	190
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	191 if __name__ == '__main__':
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	192
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	193 parser = setup_argument_parser()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	194 args = parser.parse_args()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	195
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	196 assert os.path.exists(args.in_annot), "--annot file \"%s\" not found" % (args.in_annot)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	197 assert os.path.exists(args.in_matrix), "--matrix file \"%s\" not found" % (args.in_matrix)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	198 assert os.path.exists(args.in_info), "--info file \"%s\" not found" % (args.in_info)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	199 assert os.path.exists(args.ds_markdown), "--ds-markdown file \"%s\" not found" % (args.ds_markdown)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	200
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	201 # Input files.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	202 annot_in = os.path.abspath(args.in_annot)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	203 matrix_in = os.path.abspath(args.in_matrix)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	204 info_in = os.path.abspath(args.in_info)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	205 md_in = os.path.abspath(args.ds_markdown)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	206
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	207 # Sum Sanity Checks.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	208 matrix_ids = {}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	209
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	210 with open(matrix_in) as f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	211 for line in f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	212 cols = line.strip().split("\t")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	213 for c in cols[1:]:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	214 matrix_ids[c] = 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	215 break
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	216 f.closed
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	217
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	218 assert matrix_ids, "no dataset columns found in count table file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	219
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	220 info_ids = {}
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	221
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	222 with open(info_in) as f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	223 for line in f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	224 if re.search("^Sample name", line):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	225 continue
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	226 cols = line.strip().split("\t")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	227 if cols[0] == "Sample name":
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	228 continue
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	229 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	230 info_ids[cols[0]] = 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	231 f.closed
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	232
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	233 assert info_ids, "no dataset columns found in info table file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	234 assert len(matrix_ids) == len(info_ids), "differing numbers of dataset IDs in count table and info table file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	235 assert check_two_dic_same_keys(matrix_ids, info_ids), "dataset IDs in count table and info table file not identical"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	236 assert args.ds_ms <= len(matrix_ids), "set DEWSeq min_sample > number of data samples in count / info table files (%i > %i)" % (args.ds_ms, len(matrix_ids))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	237 print("Dataset IDs are valid ... ")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	238
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	239 # Output folder.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	240 if not os.path.exists(args.out_folder):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	241 os.makedirs(args.out_folder)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	242
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	243 # Output files.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	244 abs_path_out = os.path.abspath(args.out_folder)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	245
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	246 # Copy markdown file to results folder.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	247 if args.copy_markdown:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	248 md_source = md_in
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	249 md_in = abs_path_out + "/analyseStudy.Rmd"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	250 if not os.path.exists(md_in):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	251 print("Copying markdown file to output folder ... ")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	252 shutil.copyfile(md_source, md_in)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	253
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	254 html_out = abs_path_out + "/report.html"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	255 win_csv_out = abs_path_out + "/windows.csv"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	256 sig_reg_csv_out = abs_path_out + "/significant_regions.csv"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	257 sig_win_reg_bed_out = abs_path_out + "/significant_windows_and_regions.bed"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	258 sig_reg_bed_out = abs_path_out + "/significant_regions.bed"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	259
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	260 # Delete existing files (as if no peaks found old files would be reported).
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	261 if os.path.exists(html_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	262 os.remove(html_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	263 if os.path.exists(win_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	264 os.remove(win_csv_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	265 if os.path.exists(sig_reg_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	266 os.remove(sig_reg_csv_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	267 if os.path.exists(sig_win_reg_bed_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	268 os.remove(sig_win_reg_bed_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	269 if os.path.exists(sig_reg_bed_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	270 os.remove(sig_reg_bed_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	271
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	272 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	273 Run DEWSeq R markdown file.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	274
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	275 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	276
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	277 md_ihw = "TRUE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	278 md_df = "TRUE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	279 md_lrt = "FALSE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	280 md_olc = "FALSE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	281 if args.ds_disable_ihw:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	282 md_ihw = "FALSE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	283 if args.ds_disable_df:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	284 md_df = "FALSE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	285 if args.ds_use_lrt:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	286 md_lrt = "TRUE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	287 if args.ds_use_oc:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	288 md_olc = "TRUE"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	289
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	290 md_cmd = "Rscript -e 'rmarkdown::render("
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	291 md_cmd += 'input = "%s", ' % (md_in)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	292 md_cmd += 'output_file = "%s", ' % (html_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	293 md_cmd += 'params = list(protein = "%s", ' % (args.ds_id)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	294 md_cmd += 'sampleinfo_file = "%s", ' % (info_in)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	295 md_cmd += 'countmatrix_file = "%s", ' % (matrix_in)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	296 md_cmd += 'annotation_file = "%s", ' % (annot_in)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	297 md_cmd += 'output_windows_file = "%s", ' % (win_csv_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	298 md_cmd += 'output_regions_file = "%s", ' % (sig_reg_csv_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	299 md_cmd += 'output_bed_file = "%s", ' % (sig_win_reg_bed_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	300 md_cmd += 'min_count = %i, ' % (args.ds_mc)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	301 md_cmd += 'min_sample = %i, ' % (args.ds_ms)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	302 md_cmd += 'p_value_cutoff = %s, ' % (str(args.ds_pvc))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	303 md_cmd += 'lfc_cutoff = %s, ' % (str(args.ds_lfcc))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	304 md_cmd += 'overlap_correction = %s, ' % (md_olc)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	305 md_cmd += 'IHW = %s, ' % (md_ihw)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	306 md_cmd += 'decide_fit = %s, ' % (md_df)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	307 md_cmd += 'LRT = %s))' % (md_lrt)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	308 md_cmd += "'"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	309
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	310 print("Running DEWSeq R markdown file ... ")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	311 print(md_cmd)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	312 output = subprocess.getoutput(md_cmd)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	313 print(output)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	314
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	315 print("")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	316 print("Checking for output files ... ")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	317 if os.path.exists(html_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	318 print("FOUND HTML report file \"%s\" ... " % (html_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	319 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	320 print("MISSING HTML report file \"%s\" ... " % (html_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	321 if os.path.exists(win_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	322 print("FOUND windows CSV file \"%s\" ... " % (win_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	323 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	324 print("MISSING windows CSV file \"%s\" ... " % (win_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	325 if os.path.exists(sig_reg_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	326 print("FOUND significant regions CSV file \"%s\" ... " % (sig_reg_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	327 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	328 print("MISSING significant regions CSV file \"%s\" ... " % (sig_reg_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	329
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	330 assert os.path.exists(html_out) and os.path.exists(win_csv_out), "DEWSeq terminated / did no produce any output files. This could be due to too strict filter settings (e.g., min_sample, min_count ... ). Please try again with more relaxed settings"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	331 assert os.path.exists(html_out), "output file \"%s\" not found" % (html_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	332 assert os.path.exists(win_csv_out), "output file \"%s\" not found" % (win_csv_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	333
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	334 print("")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	335 if not os.path.exists(sig_reg_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	336 print("WARNING: no significant regions found! (missing \"%s\" file)" % (sig_reg_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	337 else:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	338 assert os.path.exists(sig_win_reg_bed_out), "output file \"%s\" not found" % (sig_win_reg_bed_out)
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	339 c_sig_reg = count_file_rows(sig_reg_csv_out) - 1
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	340 print("# significant regions: %i" % (c_sig_reg))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	341 # Save contiguous BED regions in separate file.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	342 OUTBED = open(sig_reg_bed_out, "w")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	343 with open(sig_reg_csv_out) as f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	344 for line in f:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	345 row = line.strip()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	346 cols = line.strip().split("\t")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	347 if cols[1] == "region_begin":
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	348 continue
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	349 chr_id = cols[0]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	350 reg_s = cols[1]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	351 reg_e = cols[2]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	352 pol = cols[3]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	353 win_in_reg = int(cols[4])
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	354 padj_mean = cols[7]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	355 logfc_mean = cols[10]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	356 reg_id = cols[12]
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	357 new_reg_id = reg_id
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	358 # For regions consisting of > 1 window.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	359 if win_in_reg > 1:
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	360 new_reg_id = reg_id + "@region"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	361 # Print out BED with additional columns (padj, logfc).
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	362 OUTBED.write("%s\t%s\t%s\t%s\t0\t%s\t%s\t%s\n" % (chr_id, reg_s, reg_e, new_reg_id, pol, padj_mean, logfc_mean))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	363
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	364 f.closed
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	365 OUTBED.close()
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	366
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	367 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	368 Report.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	369
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	370 """
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	371
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	372 print("")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	373 print("OUTPUT FILES")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	374 print("============")
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	375 print("HTML report:\n%s" % (html_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	376 print("Windows CSV:\n%s" % (win_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	377 if os.path.exists(sig_reg_csv_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	378 print("Significant regions CSV:\n%s" % (sig_reg_csv_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	379 if os.path.exists(sig_win_reg_bed_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	380 print("Significant windows + regions BED:\n%s" % (sig_win_reg_bed_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	381 if os.path.exists(sig_reg_bed_out):
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	382 print("Significant regions BED:\n%s" % (sig_reg_bed_out))
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776" rnateam parents: diff changeset	383 print("")

Mercurial > repos > rnateam > dewseq

annotate dewseq_wrapper.py @ 0:e1cb2e012307 draft default tip