macs21: macs21_wrapper.py annotate

annotate macs21_wrapper.py @ 8:78c15c0a96ae draft

Uploaded new version with minor fixes and updates to help text.

author	pjbriggs
date	Tue, 21 Apr 2015 10:33:52 -0400
parents	0c6b14f3fefc
children	4e85d68a2347

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
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	64 $ bedGraphToBigWig treat.clipped mm9.chrom.sizes treat.bw
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	65
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	66 Get the binaries from
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	67 http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	68
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	69 We skip the fetchChromSizes step if the 'chrom_sizes'
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	70 argument supplied a valid file with the chromosome sizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	71 for the genome build in question.
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	72
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 print "Generating bigWig from bedGraph..."
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	75 # Check for chromosome sizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	76 if not os.path.exists(chrom_sizes):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	77 # Determine genome build
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	78 chrom_sizes = os.path.basename(chrom_sizes)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	79 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	80 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	81 # 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	82 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	83 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	84 sys.exit(1)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	85 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	86 # Run fetchChromSizes
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	87 chrom_sizes = os.path.join(working_dir,chrom_sizes)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	88 stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr")
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	89 cmd = "fetchChromSizes %s" % genome_build
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	90 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	91 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	92 stdout=open(chrom_sizes,'wb'),
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	93 stderr=open(stderr_file,'wb'))
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	94 proc.wait()
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	95 # Copy stderr from fetchChromSizes for information only
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	96 for line in open(stderr_file,'r'):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	97 print line.strip()
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	98 os.remove(stderr_file)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	99 # Check that the sizes file was downloaded
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	100 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	101 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	102 sys.exit(1)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	103 # Run bedClip
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	104 treat_clipped = "%s.clipped" % os.path.basename(bedgraph_file)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	105 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	106 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	107 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	108 proc.wait()
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	109 # Check that clipped file exists
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	110 treat_clipped = os.path.join(working_dir,treat_clipped)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	111 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	112 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	113 sys.exit(1)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	114 # Run bedGraphToBigWig
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	115 cmd = "bedGraphToBigWig %s %s %s" % (treat_clipped,chrom_sizes,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	116 bigwig_file)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	117 print "Running %s" % cmd
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	118 proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir)
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	119 proc.wait()
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	120 # Clean up temporary chrom length file
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	121 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	122 print "Removing temporary chrom sizes file"
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 7 diff changeset	123 os.remove(chrom_sizes)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	124
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	125 if __name__ == "__main__":
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	126
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	127 # Echo the command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	128 print ' '.join(sys.argv)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	129
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	130 # Initialise output files - values are set by reading from
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	131 # the command line supplied by the Galaxy wrapper
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	132 output_extra_html = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	133 output_extra_path = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	134 output_broadpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	135 output_gappedpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	136 output_narrowpeaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	137 output_treat_pileup = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	138 output_lambda_bedgraph = None
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	139 output_bigwig = None
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	140 output_xls_to_interval_peaks_file = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	141 output_peaks = None
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	142 output_bdgcmp = None
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	143
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	144 # Other initialisations
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	145 chrom_sizes_file = None
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	146
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	147 # Build the MACS 2.1 command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	148 # 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	149 cmdline = ["macs2 %s -t %s" % (sys.argv[1],sys.argv[2])]
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	150
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	151 # Process remaining args
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	152 for arg in sys.argv[3:]:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	153 if arg.startswith('--format='):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	154 # Convert format to uppercase
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	155 format_ = arg.split('=')[1].upper()
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	156 cmdline.append("--format=%s" % format_)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	157 elif arg.startswith('--name='):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	158 # Replace whitespace in name with underscores
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	159 experiment_name = '_'.join(arg.split('=')[1].split())
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	160 cmdline.append("--name=%s" % experiment_name)
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	161 elif arg.startswith('--length='):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	162 # Extract chromosome size file
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	163 chrom_sizes_file = arg.split('=')[1]
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	164 elif arg.startswith('--output-'):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	165 # Handle destinations for output files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	166 arg0,filen = arg.split('=')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	167 if arg0 == '--output-summits':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	168 output_summits = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	169 elif arg0 == '--output-extra-files':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	170 output_extra_html = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	171 elif arg0 == '--output-extra-files-path':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	172 output_extra_path = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	173 elif arg0 == '--output-broadpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	174 output_broadpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	175 elif arg0 == '--output-gappedpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	176 output_gappedpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	177 elif arg0 == '--output-narrowpeaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	178 output_narrowpeaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	179 elif arg0 == '--output-pileup':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	180 output_treat_pileup = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	181 elif arg0 == '--output-lambda-bedgraph':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	182 output_lambda_bedgraph = filen
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	183 elif arg0 == '--output-bigwig':
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	184 output_bigwig = filen
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	185 elif arg0 == '--output-xls-to-interval':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	186 output_xls_to_interval_peaks_file = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	187 elif arg0 == '--output-peaks':
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	188 output_peaks = filen
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	189 else:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	190 # Pass remaining args directly to MACS
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	191 # command line
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	192 cmdline.append(arg)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	193
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	194 cmdline = ' '.join(cmdline)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	195 print "Generated command line:\n%s" % cmdline
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	196
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	197 # Execute MACS2
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	198 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	199 # Make a working directory
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	200 working_dir = tempfile.mkdtemp()
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	201 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	202 # Collect stderr in a file for reporting later
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	203 stderr_filen = tempfile.NamedTemporaryFile().name
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	204 #
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	205 # Run MACS2
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	206 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	207 stderr=open(stderr_filen,'wb'))
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	208 proc.wait()
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	209
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	210 # Run R script to create PDF from model script
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	211 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	212 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	213 (experiment_name, experiment_name)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	214 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	215 proc.wait()
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	216
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	217 # Convert XLS to interval, if requested
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	218 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	219 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	220 if os.path.exists(peaks_xls_file):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	221 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	222 header='peaks file')
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	223
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	224 # Create bigWig from bedGraph, if requested
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	225 if output_bigwig is not None:
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	226 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	227 if os.path.exists(treat_bedgraph_file):
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	228 make_bigwig_from_bedgraph(treat_bedgraph_file,output_bigwig,
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	229 chrom_sizes_file,working_dir)
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	230
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	231 # 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	232 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	233 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	234 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	235 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	236 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	237 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	238 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	239 move_file(working_dir,"bdgcmp_out.bdg",output_bdgcmp)
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	240
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	241 # 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	242 # 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	243 html_file = open(output_extra_html,'wb')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	244 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	245 # Make the 'extra files' directory
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	246 os.mkdir(output_extra_path)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	247 # Move the files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	248 for filen in sorted(os.listdir(working_dir)):
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	249 shutil.move(os.path.join(working_dir,filen),
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	250 os.path.join(output_extra_path,filen))
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	251 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	252 # All files moved, close out HTML
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	253 html_file.write( '</ul></p>\n' )
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	254 # Append any stderr output
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	255 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	256 open(stderr_filen,'rb').read())
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	257 html_file.write('</body></html>\n')
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	258 html_file.close()
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	259
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	260 # Clean up the working directory and files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	261 os.unlink(stderr_filen)
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	262 os.rmdir(working_dir)

Mercurial > repos > pjbriggs > macs21

annotate macs21_wrapper.py @ 8:78c15c0a96ae draft