macs21: macs21_wrapper.py annotate

annotate macs21_wrapper.py @ 21:228d8669c559 draft

Uploaded

author	pjbriggs
date	Tue, 20 Mar 2018 11:18:29 -0400
parents	4e85d68a2347
children

rev	line source
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	1 #!/bin/env python
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	2 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	3 # Galaxy wrapper to run MACS 2.1
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	4 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	5 # Completely rewritten from the original macs2 wrapped by Ziru Zhou
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	6 # taken from http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	7
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	8 import sys
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	9 import os
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	10 import subprocess
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	11 import tempfile
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	12 import shutil
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	13
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	14 def move_file(working_dir,name,destination):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	15 """Move a file 'name' from 'working_dir' to 'destination'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	16
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	17 """
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	18 if destination is None:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	19 # Nothing to do
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	20 return
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	21 source = os.path.join(working_dir,name)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	22 if os.path.exists(source):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	23 shutil.move(source,destination)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	24
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	25 def convert_xls_to_interval(xls_file,interval_file,header=None):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	26 """Convert MACS XLS file to interval
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	27
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	28 From the MACS readme: "Coordinates in XLS is 1-based which is different with
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	29 BED format."
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	30
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	31 However this function no longer performs any coordinate conversions, it
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	32 simply ensures that any blank or non-data lines are commented out
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	33
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	34 """
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	35 fp = open(interval_file,'wb')
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	36 if header:
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	37 fp.write('#%s\n' % header)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	38 for line in open(xls_file):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	39 # Keep all existing comment lines
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	40 if line.startswith('#'):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	41 fp.write(line)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	42 else:
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	43 # Split line into fields and test to see if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	44 # the 'start' field is actually an integer
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	45 fields = line.split('\t')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	46 if len(fields) > 1:
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	47 try:
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	48 int(fields[1])
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	49 except ValueError:
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	50 # Integer conversion failed so comment out
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	51 # "bad" line instead
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	52 fields[0] = "#%s" % fields[0]
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	53 fp.write( '\t'.join( fields ) )
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	54 fp.close()
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	55
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	56 def make_bigwig_from_bedgraph(bedgraph_file,bigwig_file,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	57 chrom_sizes,working_dir=None):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	58 """Make bigWig file from a bedGraph
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	59
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	60 The protocol is:
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	61
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	62 $ fetchChromSizes.sh mm9 > mm9.chrom.sizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	63 $ bedClip treat.bedgraph mm9.chrom.sizes treat.clipped
18 4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	64 $ bedSort treat.clipped treat.clipped.sorted
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	65 $ bedGraphToBigWig treat.clipped.sorted mm9.chrom.sizes treat.bw
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	66
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	67 Get the binaries from
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	68 http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	69
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	70 We skip the fetchChromSizes step if the 'chrom_sizes'
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	71 argument supplied a valid file with the chromosome sizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	72 for the genome build in question.
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	73
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	74 """
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	75 print "Generating bigWig from bedGraph..."
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	76 # Check for chromosome sizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	77 if not os.path.exists(chrom_sizes):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	78 # Determine genome build
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	79 chrom_sizes = os.path.basename(chrom_sizes)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	80 genome_build = chrom_sizes.split('.')[0]
7 0c6b14f3fefc Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build. pjbriggs parents: 2 diff changeset	81 if genome_build == '?':
0c6b14f3fefc Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build. pjbriggs parents: 2 diff changeset	82 # No genome build set
0c6b14f3fefc Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build. pjbriggs parents: 2 diff changeset	83 sys.stderr.write("ERROR genome build not set, cannot get sizes for '?'\n")
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	84 sys.stderr.write("Assign a genome build to your input dataset and rerun\n")
7 0c6b14f3fefc Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build. pjbriggs parents: 2 diff changeset	85 sys.exit(1)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	86 print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	87 # Run fetchChromSizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	88 chrom_sizes = os.path.join(working_dir,chrom_sizes)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	89 stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr")
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	90 cmd = "fetchChromSizes %s" % genome_build
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	91 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	92 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	93 stdout=open(chrom_sizes,'wb'),
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	94 stderr=open(stderr_file,'wb'))
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	95 proc.wait()
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	96 # Copy stderr from fetchChromSizes for information only
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	97 for line in open(stderr_file,'r'):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	98 print line.strip()
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	99 os.remove(stderr_file)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	100 # Check that the sizes file was downloaded
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	101 if not os.path.exists(chrom_sizes):
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	102 sys.stderr.write("Failed to download chrom sizes for '%s'\n" % genome_build)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	103 sys.exit(1)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	104 # Run bedClip
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	105 treat_clipped = "%s.clipped" % os.path.basename(bedgraph_file)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	106 cmd = "bedClip %s %s %s" % (bedgraph_file,chrom_sizes,treat_clipped)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	107 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	108 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	109 proc.wait()
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	110 # Check that clipped file exists
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	111 treat_clipped = os.path.join(working_dir,treat_clipped)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	112 if not os.path.exists(treat_clipped):
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	113 sys.stderr.write("Failed to create clipped bed file\n")
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	114 sys.exit(1)
18 4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	115 # Run bedSort
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	116 treat_clipped_sorted = "%s.sorted" % os.path.basename(treat_clipped)
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	117 cmd = "bedSort %s %s" % (treat_clipped,treat_clipped_sorted)
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	118 print "Running %s" % cmd
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	119 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir)
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	120 proc.wait()
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	121 # Check that sorted file exists
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	122 treat_clipped_sorted = os.path.join(working_dir,treat_clipped_sorted)
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	123 if not os.path.exists(treat_clipped_sorted):
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	124 sys.stderr.write("Failed to create sorted clipped bed file\n")
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	125 sys.exit(1)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	126 # Run bedGraphToBigWig
18 4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	127 cmd = "bedGraphToBigWig %s %s %s" % (treat_clipped_sorted,
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	128 chrom_sizes,
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	129 bigwig_file)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	130 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	131 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	132 proc.wait()
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	133 # Clean up temporary chrom length file
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	134 if os.path.dirname(chrom_sizes) == working_dir:
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	135 print "Removing temporary chrom sizes file"
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	136 os.remove(chrom_sizes)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	137
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	138 if __name__ == "__main__":
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	139
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	140 # Echo the command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	141 print ' '.join(sys.argv)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	142
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	143 # Initialise output files - values are set by reading from
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	144 # the command line supplied by the Galaxy wrapper
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	145 output_extra_html = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	146 output_extra_path = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	147 output_broadpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	148 output_gappedpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	149 output_narrowpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	150 output_treat_pileup = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	151 output_lambda_bedgraph = None
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	152 output_bigwig = None
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	153 output_xls_to_interval_peaks_file = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	154 output_peaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	155 output_bdgcmp = None
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	156
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	157 # Other initialisations
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	158 chrom_sizes_file = None
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	159
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	160 # Build the MACS 2.1 command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	161 # Initial arguments are always the same: command & input ChIP-seq file name
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	162 cmdline = ["macs2 %s -t %s" % (sys.argv[1],sys.argv[2])]
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	163
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	164 # Process remaining args
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	165 for arg in sys.argv[3:]:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	166 if arg.startswith('--format='):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	167 # Convert format to uppercase
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	168 format_ = arg.split('=')[1].upper()
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	169 cmdline.append("--format=%s" % format_)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	170 elif arg.startswith('--name='):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	171 # Replace whitespace in name with underscores
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	172 experiment_name = '_'.join(arg.split('=')[1].split())
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	173 cmdline.append("--name=%s" % experiment_name)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	174 elif arg.startswith('--length='):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	175 # Extract chromosome size file
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	176 chrom_sizes_file = arg.split('=')[1]
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	177 elif arg.startswith('--output-'):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	178 # Handle destinations for output files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	179 arg0,filen = arg.split('=')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	180 if arg0 == '--output-summits':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	181 output_summits = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	182 elif arg0 == '--output-extra-files':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	183 output_extra_html = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	184 elif arg0 == '--output-extra-files-path':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	185 output_extra_path = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	186 elif arg0 == '--output-broadpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	187 output_broadpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	188 elif arg0 == '--output-gappedpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	189 output_gappedpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	190 elif arg0 == '--output-narrowpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	191 output_narrowpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	192 elif arg0 == '--output-pileup':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	193 output_treat_pileup = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	194 elif arg0 == '--output-lambda-bedgraph':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	195 output_lambda_bedgraph = filen
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	196 elif arg0 == '--output-bigwig':
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	197 output_bigwig = filen
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	198 elif arg0 == '--output-xls-to-interval':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	199 output_xls_to_interval_peaks_file = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	200 elif arg0 == '--output-peaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	201 output_peaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	202 else:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	203 # Pass remaining args directly to MACS
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	204 # command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	205 cmdline.append(arg)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	206
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	207 cmdline = ' '.join(cmdline)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	208 print "Generated command line:\n%s" % cmdline
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	209
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	210 # Execute MACS2
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	211 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	212 # Make a working directory
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	213 working_dir = tempfile.mkdtemp()
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	214 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	215 # Collect stderr in a file for reporting later
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	216 stderr_filen = tempfile.NamedTemporaryFile().name
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	217 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	218 # Run MACS2
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	219 proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir,
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	220 stderr=open(stderr_filen,'wb'))
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	221 proc.wait()
18 4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	222 exit_code = proc.returncode
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	223 if exit_code != 0:
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	224 sys.stderr.write(open(stderr_filen,'rb').read())
4e85d68a2347 Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2. pjbriggs parents: 8 diff changeset	225 sys.exit(exit_code)
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	226
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	227 # Run R script to create PDF from model script
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	228 if os.path.exists(os.path.join(working_dir,"%s_model.r" % experiment_name)):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	229 cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % \
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	230 (experiment_name, experiment_name)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	231 proc = subprocess.Popen(args=cmdline,shell=True,cwd=working_dir)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	232 proc.wait()
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	233
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	234 # Convert XLS to interval, if requested
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	235 if output_xls_to_interval_peaks_file is not None:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	236 peaks_xls_file = os.path.join(working_dir,'%s_peaks.xls' % experiment_name )
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	237 if os.path.exists(peaks_xls_file):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	238 convert_xls_to_interval(peaks_xls_file,output_xls_to_interval_peaks_file,
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	239 header='peaks file')
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	240
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	241 # Create bigWig from bedGraph, if requested
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	242 if output_bigwig is not None:
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	243 treat_bedgraph_file = os.path.join(working_dir,'%s_treat_pileup.bdg' % experiment_name)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	244 if os.path.exists(treat_bedgraph_file):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	245 make_bigwig_from_bedgraph(treat_bedgraph_file,output_bigwig,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	246 chrom_sizes_file,working_dir)
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	247
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	248 # Move MACS2 output files from working dir to their final destinations
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	249 move_file(working_dir,"%s_summits.bed" % experiment_name,output_summits)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	250 move_file(working_dir,"%s_peaks.xls" % experiment_name,output_peaks)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	251 move_file(working_dir,"%s_peaks.narrowPeak" % experiment_name,output_narrowpeaks)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	252 move_file(working_dir,"%s_peaks.broadPeak" % experiment_name,output_broadpeaks)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	253 move_file(working_dir,"%s_peaks.gappedPeak" % experiment_name,output_gappedpeaks)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	254 move_file(working_dir,"%s_treat_pileup.bdg" % experiment_name,output_treat_pileup)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	255 move_file(working_dir,"%s_control_lambda.bdg" % experiment_name,output_lambda_bedgraph)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	256 move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	257
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	258 # Move remaining file to the 'extra files' path and link from the HTML
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	259 # file to allow user to access them from within Galaxy
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	260 html_file = open(output_extra_html,'wb')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	261 html_file.write('<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	262 # Make the 'extra files' directory
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	263 os.mkdir(output_extra_path)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	264 # Move the files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	265 for filen in sorted(os.listdir(working_dir)):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	266 shutil.move(os.path.join(working_dir,filen),
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	267 os.path.join(output_extra_path,filen))
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	268 html_file.write( '<li><a href="%s">%s</a></li>\n' % (filen,filen))
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	269 # All files moved, close out HTML
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	270 html_file.write( '</ul></p>\n' )
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	271 # Append any stderr output
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	272 html_file.write('<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' %
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	273 open(stderr_filen,'rb').read())
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	274 html_file.write('</body></html>\n')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	275 html_file.close()
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	276
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	277 # Clean up the working directory and files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	278 os.unlink(stderr_filen)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	279 os.rmdir(working_dir)

Mercurial > repos > pjbriggs > macs21

annotate macs21_wrapper.py @ 21:228d8669c559 draft