comparison macs_wrapper.py @ 6:3ef6fc38df62 draft

Uploaded

5:8fe679d31b82

    output_extra_path = sys.argv[4]
    # Added peaks output argument
    output_peaks =  sys.argv[5]    
    
    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
    cmdline = "macs -t %s" % ",".join( options['input_chipseq'] )
    if options['input_control']:
        cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
    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'] )
    if 'wig' in options:
        wigextend = int( options['wig']['wigextend']  )

6:3ef6fc38df62

    output_extra_path = sys.argv[4]
    # Added peaks output argument
    output_peaks =  sys.argv[5]    
    
    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
    cmdline = "macs14 -t %s" % ",".join( options['input_chipseq'] )
    if options['input_control']:
        cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
    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'] )
    if 'wig' in options:
        wigextend = int( options['wig']['wigextend']  )