bismark: bismark_wrapper.py annotate

annotate bismark_wrapper.py @ 21:120b7b35e442 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"

author	bgruening
date	Thu, 22 Apr 2021 17:05:46 +0000
parents	bb74e17e47d7
children

rev	line source
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	1 #!/usr/bin/env python
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	2
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	3 import argparse
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	4 import fileinput
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	5 import logging
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	6 import math
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	7 import os
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	8 import shutil
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	9 import subprocess
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	10 import sys
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	11 import tempfile
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	12 from glob import glob
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	13
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	14
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	15 def stop_err(logger, msg):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	16 logger.critical(msg)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	17 sys.exit(1)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	18
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	19
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	20 def log_subprocess_output(logger, pipe):
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	21 for line in iter(pipe.readline, b""):
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	22 logger.debug(line.decode().rstrip())
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	23
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	24
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	25 def __main__():
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	26 # Parse Command Line
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	27 parser = argparse.ArgumentParser(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	28 description="Wrapper for the bismark bisulfite mapper."
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	29 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	30 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	31 "-p",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	32 "--num-threads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	33 dest="num_threads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	34 type=int,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	35 default=4,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	36 help="Use this many threads to align reads. The default is 4.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	37 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	38
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	39 # input options
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	40 parser.add_argument("--own-file", dest="own_file", help="")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	41 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	42 "-D",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	43 "--indexes-path",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	44 dest="index_path",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	45 help="Indexes directory; location of .ebwt and .fa files.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	46 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	47 parser.add_argument("-O", "--output", dest="output")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	48
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	49 parser.add_argument("--output-report-file", dest="output_report_file")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	50 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	51 "--suppress-header", dest="suppress_header", action="store_true"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	52 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	53
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	54 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	55 "--mate-paired",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	56 dest="mate_paired",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	57 action="store_true",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	58 help="Reads are mate-paired",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	59 default=False,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	60 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	61
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	62 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	63 "-1",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	64 "--mate1",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	65 dest="mate1",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	66 help="The forward reads file in Sanger FASTQ or FASTA format.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	67 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	68 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	69 "-2",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	70 "--mate2",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	71 dest="mate2",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	72 help="The reverse reads file in Sanger FASTQ or FASTA format.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	73 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	74 parser.add_argument("--sort-bam", dest="sort_bam", action="store_true")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	75
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	76 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	77 "--output-unmapped-reads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	78 dest="output_unmapped_reads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	79 help="Additional output file with unmapped reads (single-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	80 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	81 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	82 "--output-unmapped-reads-l",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	83 dest="output_unmapped_reads_l",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	84 help="File name for unmapped reads (left, paired-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	85 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	86 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	87 "--output-unmapped-reads-r",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	88 dest="output_unmapped_reads_r",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	89 help="File name for unmapped reads (right, paired-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	90 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	91
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	92 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	93 "--output-suppressed-reads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	94 dest="output_suppressed_reads",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	95 help="Additional output file with suppressed reads (single-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	96 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	97 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	98 "--output-suppressed-reads-l",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	99 dest="output_suppressed_reads_l",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	100 help="File name for suppressed reads (left, paired-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	101 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	102 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	103 "--output-suppressed-reads-r",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	104 dest="output_suppressed_reads_r",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	105 help="File name for suppressed reads (right, paired-end).",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	106 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	107 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	108 "--stdout",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	109 dest="output_stdout",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	110 help="File name for the standard output of bismark.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	111 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	112
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	113 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	114 "--single-paired",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	115 dest="single_paired",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	116 help="The single-end reads file in Sanger FASTQ or FASTA format.",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	117 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	118
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	119 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	120 "--fastq", action="store_true", help="Query filetype is in FASTQ format"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	121 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	122 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	123 "--fasta", action="store_true", help="Query filetype is in FASTA format"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	124 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	125 parser.add_argument("--phred64-quals", dest="phred64", action="store_true")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	126 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	127 "--non_directional", dest="non_directional", action="store_true"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	128 )
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	129 parser.add_argument("--pbat", dest="pbat", action="store_true")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	130
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	131 parser.add_argument("--skip-reads", dest="skip_reads", type=int)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	132 parser.add_argument("--score-min", dest="score_min", type=str)
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	133 parser.add_argument("--qupto", type=int)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	134
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	135 # paired end options
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	136 parser.add_argument("-I", "--minins", dest="min_insert")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	137 parser.add_argument("-X", "--maxins", dest="max_insert")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	138 parser.add_argument("--no-mixed", dest="no_mixed", action="store_true")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	139 parser.add_argument("--no-discordant", dest="no_discordant", action="store_true")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	140
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	141 # parse general options
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	142 # default 20
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	143 parser.add_argument("--seed-len", dest="seed_len", type=int)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	144 # default 15
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	145 parser.add_argument(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	146 "--seed-extention-attempts", dest="seed_extention_attempts", type=int
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	147 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	148 # default 0
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	149 parser.add_argument("--seed-mismatches", dest="seed_mismatches", type=int)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	150 # default 2
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	151 parser.add_argument("--max-reseed", dest="max_reseed", type=int)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	152
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	153 """
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	154 The number of megabytes of memory a given thread is given to store path
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	155 descriptors in --best mode. Best-first search must keep track of many paths
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	156 at once to ensure it is always extending the path with the lowest cumulative
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	157 cost. Bowtie tries to minimize the memory impact of the descriptors, but
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	158 they can still grow very large in some cases. If you receive an error message
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	159 saying that chunk memory has been exhausted in --best mode, try adjusting
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	160 this parameter up to dedicate more memory to the descriptors. Default: 512.
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	161 """
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	162 parser.add_argument("--chunkmbs", type=int, default=512)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	163
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	164 args = parser.parse_args()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	165
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	166 logger = logging.getLogger("bismark_wrapper")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	167 logger.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	168 ch = logging.StreamHandler(sys.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	169 if args.output_stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	170 ch.setLevel(logging.WARNING)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	171 handler = logging.FileHandler(args.output_stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	172 handler.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	173 logger.addHandler(handler)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	174 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	175 ch.setLevel(logging.DEBUG)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	176 logger.addHandler(ch)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	177
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	178 # Create bismark index if necessary.
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	179 index_dir = ""
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	180 tmp_index_dir = None
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	181 if args.own_file:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	182 logger.info(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	183 "Create a temporary index with the offered files from the user. "
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	184 "Utilizing the script: bismark_genome_preparation"
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	185 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	186 tmp_index_dir = tempfile.mkdtemp()
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	187 index_path = os.path.join(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	188 tmp_index_dir, ".".join(os.path.split(args.own_file)[1].split(".")[:-1])
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	189 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	190 try:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	191 # Create a hard link pointing to args.own_file named 'index_path'.fa.
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	192 os.symlink(args.own_file, index_path + ".fa")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	193 except Exception as e:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	194 if os.path.exists(tmp_index_dir):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	195 shutil.rmtree(tmp_index_dir)
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	196 stop_err(logger, "Error in linking the reference database!\n%s" % e)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	197 # bismark_genome_preparation needs the complete path to the folder in which the database is stored
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	198 cmd_index = ["bismark_genome_preparation", "--bowtie2", tmp_index_dir]
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	199 try:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	200 logger.info("Generating index with: '%s'", " ".join(cmd_index))
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	201 process = subprocess.Popen(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	202 cmd_index, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	203 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	204 with process.stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	205 log_subprocess_output(logger, process.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	206 exitcode = process.wait()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	207 if exitcode != 0:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	208 raise Exception(process.stderr)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	209 except Exception as e:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	210 if os.path.exists(tmp_index_dir):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	211 shutil.rmtree(tmp_index_dir)
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	212 stop_err(logger, "Error indexing reference sequence!\n%s" % e)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	213 index_dir = tmp_index_dir
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	214 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	215 # bowtie path is the path to the index directory and the first path of the index file name
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	216 index_dir = os.path.dirname(args.index_path)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	217
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	218 # Build bismark command
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	219 tmp_bismark_dir = tempfile.mkdtemp()
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	220 output_dir = os.path.join(tmp_bismark_dir, "results")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	221 cmd = [
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	222 "bismark",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	223 "--bam",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	224 "--temp_dir",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	225 tmp_bismark_dir,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	226 "-o",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	227 output_dir,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	228 "--quiet",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	229 ]
17 aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde" bgruening parents: 16 diff changeset	230 if not args.pbat:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	231 cmd.append("--gzip")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	232
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	233 if args.fasta:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	234 # the query input files (specified as mate1,mate2 or singles) are FastA
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	235 cmd.append("--fasta")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	236 elif args.fastq:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	237 cmd.append("--fastq")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	238
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	239 # alignment options
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	240 if args.num_threads > 2:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	241 # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	242 cmd.extend(["-p", str(int(math.floor(args.num_threads / 2)))])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	243 if args.seed_mismatches:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	244 cmd.extend(["-N", str(args.seed_mismatches)])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	245 if args.seed_len:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	246 cmd.extend(["-L", str(args.seed_len)])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	247 if args.seed_extention_attempts:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	248 cmd.extend(["-D", str(args.seed_extention_attempts)])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	249 if args.max_reseed:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	250 cmd.extend(["-R", str(args.max_reseed)])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	251 if args.no_discordant:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	252 cmd.append("--no-discordant")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	253 if args.no_mixed:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	254 cmd.append("--no-mixed")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	255 if args.skip_reads:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	256 cmd.extend(["--skip", str(args.skip_reads)])
16 a4504327c890 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c" bgruening parents: 10 diff changeset	257 if args.score_min:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	258 cmd.extend(["--score_min", str(args.score_min)])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	259 if args.qupto:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	260 cmd.extend(["--upto", "args.qupto"])
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	261 if args.phred64:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	262 cmd.append("--phred64-quals")
10 7bffcb6fc81d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b bgruening parents: 8 diff changeset	263 if args.non_directional:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	264 cmd.append("--non_directional")
17 aa9bf0f29a9f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde" bgruening parents: 16 diff changeset	265 if args.pbat:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	266 cmd.append("--pbat")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	267 if args.suppress_header:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	268 cmd.append("--sam-no-hd")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	269 if args.output_unmapped_reads or (
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	270 args.output_unmapped_reads_l and args.output_unmapped_reads_r
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	271 ):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	272 cmd.append("--un")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	273 if args.output_suppressed_reads or (
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	274 args.output_suppressed_reads_l and args.output_suppressed_reads_r
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	275 ):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	276 cmd.append("--ambiguous")
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	277
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	278 cmd.append(index_dir)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	279 # Set up the reads
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	280 if args.mate_paired:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	281 # paired-end reads library
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	282 cmd.extend(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	283 [
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	284 "-1",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	285 args.mate1,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	286 "-2",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	287 args.mate2,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	288 "-I",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	289 str(args.min_insert),
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	290 "-X",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	291 str(args.max_insert),
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	292 ]
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	293 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	294 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	295 # single paired reads library
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	296 cmd.append(args.single_paired)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	297
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	298 # Run
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	299 try:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	300 logger.info("Running bismark with: '%s'", " ".join(cmd))
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	301 process = subprocess.Popen(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	302 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	303 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	304 with process.stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	305 log_subprocess_output(logger, process.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	306 exitcode = process.wait()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	307 if exitcode != 0:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	308 raise Exception(process.stderr)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	309 except Exception as e:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	310 stop_err(logger, "Error in running bismark!\n%s" % e)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	311
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	312 # collect and copy output files
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	313 if args.output_report_file:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	314 output_report_file = open(args.output_report_file, "w+")
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	315 for line in fileinput.input(glob(os.path.join(output_dir, "*report.txt"))):
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	316 output_report_file.write(line)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	317 output_report_file.close()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	318
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	319 if args.output_suppressed_reads:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	320 if glob(os.path.join(output_dir, "ambiguous_reads.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	321 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	322 glob(os.path.join(output_dir, "ambiguous_reads."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	323 args.output_suppressed_reads,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	324 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	325 if args.output_suppressed_reads_l:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	326 if glob(os.path.join(output_dir, "ambiguous_reads_1.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	327 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	328 glob(os.path.join(output_dir, "ambiguous_reads_1."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	329 args.output_suppressed_reads_l,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	330 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	331 if args.output_suppressed_reads_r:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	332 if glob(os.path.join(output_dir, "ambiguous_reads_2.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	333 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	334 glob(os.path.join(output_dir, "ambiguous_reads_2."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	335 args.output_suppressed_reads_r,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	336 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	337
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	338 if args.output_unmapped_reads:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	339 if glob(os.path.join(output_dir, "unmapped_reads.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	340 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	341 glob(os.path.join(output_dir, "unmapped_reads."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	342 args.output_unmapped_reads,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	343 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	344 if args.output_unmapped_reads_l:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	345 if glob(os.path.join(output_dir, "unmapped_reads_1.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	346 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	347 glob(os.path.join(output_dir, "unmapped_reads_1."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	348 args.output_unmapped_reads_l,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	349 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	350 if args.output_unmapped_reads_r:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	351 if glob(os.path.join(output_dir, "unmapped_reads_2.")):
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	352 shutil.move(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	353 glob(os.path.join(output_dir, "unmapped_reads_2."))[0],
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	354 args.output_unmapped_reads_r,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	355 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	356
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	357 try:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	358 # merge all bam files
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	359 tmp_res = tempfile.NamedTemporaryFile(dir=output_dir).name
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	360
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	361 bam_files = glob(os.path.join(output_dir, "*.bam"))
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	362 if len(bam_files) > 1:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	363 cmd = [
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	364 "samtools",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	365 "merge",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	366 "-@",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	367 str(args.num_threads),
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	368 "-f",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	369 tmp_res
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	370 ]
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	371 [cmd.append(x) for x in bam_files]
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	372 logger.info("Merging bams with: '%s'", cmd)
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	373 process = subprocess.Popen(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	374 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	375 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	376 with process.stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	377 log_subprocess_output(logger, process.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	378 exitcode = process.wait()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	379 if exitcode != 0:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	380 raise Exception(process.stderr)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	381 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	382 tmp_res = bam_files[0]
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	383
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	384 bam_path = "%s" % tmp_res
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	385
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	386 if os.path.exists(bam_path):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	387 if args.sort_bam:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	388 cmd = [
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	389 "samtools",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	390 "sort",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	391 "-@",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	392 str(args.num_threads),
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	393 bam_path,
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	394 "sorted_bam",
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	395 ]
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	396 logger.info("Sorting bam with: '%s'", cmd)
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	397 process = subprocess.Popen(
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	398 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	399 )
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	400 with process.stdout:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	401 log_subprocess_output(logger, process.stdout)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	402 exitcode = process.wait()
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	403 if exitcode != 0:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	404 raise Exception(process.stderr)
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	405 shutil.move("sorted_bam.bam", args.output)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	406 else:
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	407 shutil.move(bam_path, args.output)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	408 else:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	409 stop_err(logger, "BAM file no found:\n%s" % bam_path)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	410
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	411 except Exception as e:
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	412 stop_err(logger, "Error in merging bam files!\n%s" % e)
8 9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	413
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	414 # Clean up temp dirs
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	415 if tmp_index_dir and os.path.exists(tmp_index_dir):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	416 shutil.rmtree(tmp_index_dir)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	417 if os.path.exists(tmp_bismark_dir):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	418 shutil.rmtree(tmp_bismark_dir)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	419 if os.path.exists(output_dir):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	420 shutil.rmtree(output_dir)
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	421
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff bgruening parents: diff changeset	422
21 120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	423 if __name__ == "__main__":
120b7b35e442 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798" bgruening parents: 18 diff changeset	424 __main__()

Mercurial > repos > bgruening > bismark

annotate bismark_wrapper.py @ 21:120b7b35e442 draft