def run( o_options ):
"""The Main function/pipeline for duplication filter.
"""
# Parse options...
options = opt_validate( o_options )
# end of parsing commandline options
info = options.info
warn = options.warn
debug = options.debug
error = options.error
outputfile = open(options.oprefix+"_refinepeak.bed", "w")
peakio = file(options.bedfile)
peaks = PeakIO()
for l in peakio:
fs = l.rstrip().split()
peaks.add( fs[0], int(fs[1]), int(fs[2]), name=fs[3] )
peaks.sort()
#1 Read tag files
info("read tag files...")
fwtrack = load_tag_files_options (options)
retval = fwtrack.compute_region_tags_from_peaks( peaks, find_summit, window_size = options.windowsize, cutoff = options.cutoff )
outputfile.write( "\n".join( map(lambda x: "%s\t%d\t%d\t%s\t%.2f" % x , retval) ) )
info("Done!")
info("Check output file: %s" % options.oprefix+"_refinepeak.bed")
def run( o_options ):
"""The Main function/pipeline for duplication filter.
"""
# Parse options...
options = opt_validate( o_options )
# end of parsing commandline options
info = options.info
warn = options.warn
debug = options.debug
error = options.error
outputfile = open(options.oprefix+"_refinepeak.bed", "w")
#if options.outputfile != "stdout":
# assert not os.path.exists(options.outputfile), "%s already exists, please check!" % options.outputfile
# outfhd = open(options.outputfile,"w")
#else:
# outfhd = sys.stdout
peakio = file(options.bedfile)
peaks = PeakIO()
for l in peakio:
fs = l.rstrip().split()
peaks.add( fs[0], int(fs[1]), int(fs[2]), name=fs[3] )
peaks.sort()
#for l in peakio:
#l = peakio.readline()
#fs = l.rstrip().split()
#print fs
#1 Read tag files
info("read tag files...")
fwtrack = load_tag_files_options (options)
#info("tag size = %d" % options.tsize)
#fwtrack.fw = options.tsize
retval = fwtrack.compute_region_tags_from_peaks( peaks, find_summit, window_size = options.windowsize, cutoff = options.cutoff )
outputfile.write( "\n".join( map(lambda x: "%s\t%d\t%d\t%s\t%.2f" % x , retval) ) )
info("Done!")
info("Check output file: %s" % options.oprefix+"_refinepeak.bed")
