0
+ − 1 import glob
+ − 2 import gzip
+ − 3 import json
+ − 4 import os
+ − 5 import os.path
+ − 6 import shutil
+ − 7 import subprocess
+ − 8 import sys
+ − 9 import tempfile
+ − 10
+ − 11 CHUNK_SIZE = 1024
+ − 12
+ − 13 def gunzip_cat_glob_path( glob_path, target_filename, delete = False ):
+ − 14 out = open( target_filename, 'wb' )
+ − 15 for filename in glob.glob( glob_path ):
+ − 16 fh = gzip.open( filename, 'rb' )
+ − 17 while True:
+ − 18 data = fh.read( CHUNK_SIZE )
+ − 19 if data:
+ − 20 out.write( data )
+ − 21 else:
+ − 22 break
+ − 23 fh.close()
+ − 24 if delete:
+ − 25 os.unlink( filename )
+ − 26 out.close()
+ − 27
+ − 28 def xls_to_interval( xls_file, interval_file, header = None ):
+ − 29 out = open( interval_file, 'wb' )
+ − 30 if header:
+ − 31 out.write( '#%s\n' % header )
+ − 32 wrote_header = False
+ − 33 #From macs readme: Coordinates in XLS is 1-based which is different with BED format.
+ − 34 for line in open( xls_file ):
+ − 35 #keep all existing comment lines
+ − 36 if line.startswith( '#' ):
+ − 37 out.write( line )
+ − 38 elif not wrote_header:
+ − 39 out.write( '#%s' % line )
+ − 40 wrote_header = True
+ − 41 else:
+ − 42 fields = line.split( '\t' )
+ − 43 if len( fields ) > 1:
+ − 44 fields[1] = str( int( fields[1] ) - 1 )
+ − 45 out.write( '\t'.join( fields ) )
+ − 46 out.close()
+ − 47
+ − 48 def main():
+ − 49 options = json.load( open( sys.argv[1] ) )
+ − 50 output_bed = sys.argv[2]
+ − 51 output_extra_html = sys.argv[3]
+ − 52 output_extra_path = sys.argv[4]
+ − 53
+ − 54 experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for filenames (gzip of wig files will fail with spaces - macs doesn't properly escape them)..need to replace all whitespace, split makes this easier
+ − 55 cmdline = "macs -t %s" % ",".join( options['input_chipseq'] )
+ − 56 if options['input_control']:
+ − 57 cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
+ − 58 cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] )
+ − 59 if 'wig' in options:
+ − 60 wigextend = int( options['wig']['wigextend'] )
+ − 61 if wigextend >= 0:
+ − 62 wigextend = "--wigextend='%s'" % wigextend
+ − 63 else:
+ − 64 wigextend = ''
+ − 65 cmdline = "%s --wig %s --space='%s'" % ( cmdline, wigextend, options['wig']['space'] )
+ − 66 if 'nomodel' in options:
+ − 67 cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] )
+ − 68 if 'diag' in options:
+ − 69 cmdline = "%s --diag --fe-min='%s' --fe-max='%s' --fe-step='%s'" % ( cmdline, options['diag']['fe-min'], options['diag']['fe-max'], options['diag']['fe-step'] )
+ − 70
+ − 71 tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user
+ − 72 stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report
+ − 73 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+ − 74 proc.wait()
+ − 75 #We don't want to set tool run to error state if only warnings or info, e.g. mfold could be decreased to improve model, but let user view macs log
+ − 76 #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
+ − 77 if proc.returncode:
+ − 78 stderr_f = open( stderr_name )
+ − 79 while True:
+ − 80 chunk = stderr_f.read( CHUNK_SIZE )
+ − 81 if not chunk:
+ − 82 stderr_f.close()
+ − 83 break
+ − 84 sys.stderr.write( chunk )
+ − 85
+ − 86 #run R to create pdf from model script
+ − 87 if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ):
+ − 88 cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name )
+ − 89 proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
+ − 90 proc.wait()
+ − 91
+ − 92
+ − 93 #move bed out to proper output file
+ − 94 created_bed_name = os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name )
+ − 95 if os.path.exists( created_bed_name ):
+ − 96 shutil.move( created_bed_name, output_bed )
+ − 97
+ − 98 #parse xls files to interval files as needed
+ − 99 if options['xls_to_interval']:
+ − 100 create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name )
+ − 101 if os.path.exists( create_peak_xls_file ):
+ − 102 xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' )
+ − 103 create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name )
+ − 104 if os.path.exists( create_peak_xls_file ):
+ − 105 xls_to_interval( create_peak_xls_file, options['xls_to_interval']['negative_peaks_file'], header = 'negative peaks file' )
+ − 106
+ − 107 #merge and move wig files as needed, delete gz'd files and remove emptied dirs
+ − 108 if 'wig' in options:
+ − 109 wig_base_dir = os.path.join( tmp_dir, "%s_MACS_wiggle" % experiment_name )
+ − 110 if os.path.exists( wig_base_dir ):
+ − 111 #treatment
+ − 112 treatment_dir = os.path.join( wig_base_dir, "treat" )
+ − 113 if os.path.exists( treatment_dir ):
+ − 114 gunzip_cat_glob_path( os.path.join( treatment_dir, "*.wig.gz" ), options['wig']['output_treatment_file'], delete = True )
+ − 115 os.rmdir( treatment_dir )
+ − 116 #control
+ − 117 if options['input_control']:
+ − 118 control_dir = os.path.join( wig_base_dir, "control" )
+ − 119 if os.path.exists( control_dir ):
+ − 120 gunzip_cat_glob_path( os.path.join( control_dir, "*.wig.gz" ), options['wig']['output_control_file'], delete = True )
+ − 121 os.rmdir( control_dir )
+ − 122 os.rmdir( wig_base_dir )
+ − 123
+ − 124 #move all remaining files to extra files path of html file output to allow user download
+ − 125 out_html = open( output_extra_html, 'wb' )
+ − 126 out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name )
+ − 127 os.mkdir( output_extra_path )
+ − 128 for filename in sorted( os.listdir( tmp_dir ) ):
+ − 129 shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) )
+ − 130 out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) )
+ − 131 out_html.write( '</ul></p>\n' )
+ − 132 out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() )
+ − 133 out_html.write( '</body></html>\n' )
+ − 134 out_html.close()
+ − 135
+ − 136 os.unlink( stderr_name )
+ − 137 os.rmdir( tmp_dir )
+ − 138
+ − 139 if __name__ == "__main__": main()
