def run( args ):
"""The Differential function/pipeline for MACS.
"""
# Parse options...
options = diff_opt_validate( args )
#0 output arguments
# info("\n"+options.argtxt)
ofile_prefix = options.name
# check if tag files exist
with open(options.t1bdg) as f: pass
with open(options.c1bdg) as f: pass
with open(options.t2bdg) as f: pass
with open(options.c2bdg) as f: pass
if not options.peaks1 == '':
info("Read peaks for condition 1...")
p1io = PeakIO()
with open(options.peaks1, 'rU') as f:
p1io.read_from_xls(f)
if not options.peaks2 == '':
info("Read peaks for condition 2...")
p2io = PeakIO()
with open(options.peaks2, 'rU') as f:
p2io.read_from_xls(f)
#1 Read tag files
info("Read and build treatment 1 bedGraph...")
t1bio = cBedGraphIO.bedGraphIO(options.t1bdg)
t1btrack = t1bio.build_bdgtrack()
info("Read and build control 1 bedGraph...")
c1bio = cBedGraphIO.bedGraphIO(options.c1bdg)
c1btrack = c1bio.build_bdgtrack()
if len(options.depth) >=2:
depth1 = options.depth[0]
depth2 = options.depth[1]
else:
depth1 = options.depth[0]
depth2 = depth1
info("Read and build treatment 2 bedGraph...")
t2bio = cBedGraphIO.bedGraphIO(options.t2bdg)
t2btrack = t2bio.build_bdgtrack()
info("Read and build control 2 bedGraph...")
c2bio = cBedGraphIO.bedGraphIO(options.c2bdg)
c2btrack = c2bio.build_bdgtrack()
#3 Call Peaks
diffscore = DiffScoreTrackI( t1btrack,
c1btrack,
t2btrack,
c2btrack,
depth1, depth2 )
diffscore.finalize()
if options.call_peaks:
diffscore.set_track_score_method(options.track_score_method)
info("Calling peaks")
if options.track_score_method == 'p':
diffscore.call_peaks(cutoff = options.peaks_log_pvalue,
min_length = options.pminlen)
elif options.track_score_method == 'q':
diffscore.call_peaks(cutoff = options.peaks_log_qvalue,
min_length = options.pminlen)
else:
raise NotImplementedError
else:
info("Using existing peaks")
diffscore.store_peaks(p1io, p2io)
info("Rebuilding chromosomes")
diffscore.rebuild_chromosomes()
diffscore.annotate_peaks()
info("Calling differentially occupied peaks")
if options.score_method == 'p':
diffscore.call_diff_peaks(cutoff = options.log_pvalue,
min_length = options.dminlen,
score_method = options.score_method)
if options.score_method == 'q':
diffscore.call_diff_peaks(cutoff = options.log_qvalue,
min_length = options.dminlen,
score_method = options.score_method)
# diffscore.print_some_peaks()
# diffscore.print_diff_peaks()
info("Write output xls and BED files...")
ofhd_xls = open( os.path.join( options.outdir, options.peakxls), "w" )
ofhd_xls.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls.write( options.argtxt+"\n" )
ofhd_bed = open( os.path.join( options.outdir, options.peakbed), "w" )
# pass write method so we can print too, and include name
diffscore.write_peaks(xls=ofhd_xls, bed=ofhd_bed,
name = options.name, name_prefix="%s_peak_",
description="Peaks for %s (Made with MACS v2, " + strftime("%x") + ")",
trackline=options.trackline)
ofhd_xls.close()
ofhd_bed.close()
if diffscore.has_peakio():
info("Write annotated peak xls files...")
ofhd_xls1 = open( os.path.join( options.outdir, options.peak1xls), "w" )
ofhd_xls1.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls1.write(options.argtxt+"\n")
ofhd_xls2 = open( os.path.join( options.outdir, options.peak2xls), "w" )
ofhd_xls2.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls2.write(options.argtxt+"\n")
diffscore.write_peaks_by_summit(ofhd_xls1, ofhd_xls2,
name = options.name, name_prefix="%s_peak_")
ofhd_xls1.close()
ofhd_xls2.close()
if options.store_bdg:
info("#4 Write output bedgraph files...")
ofhd_logLR = open( os.path.join( options.outdir, options.bdglogLR), "w" )
ofhd_pvalue = open( os.path.join( options.outdir, options.bdgpvalue), "w" )
ofhd_logFC = open( os.path.join( options.outdir, options.bdglogFC), "w" )
diffscore.write_bedgraphs(logLR=ofhd_logLR, pvalue=ofhd_pvalue,
logFC=ofhd_logFC, name = options.name,
description=" for %s (Made with MACS v2, " + strftime("%x") + ")",
trackline=options.trackline)
ofhd_logLR.close()
ofhd_pvalue.close()
ofhd_logFC.close()
def run( args ):
"""The Differential function/pipeline for MACS.
"""
# Parse options...
options = diff_opt_validate( args )
#0 output arguments
# info("\n"+options.argtxt)
ofile_prefix = options.name
# check if tag files exist
with open(options.t1bdg) as f: pass
with open(options.c1bdg) as f: pass
with open(options.t2bdg) as f: pass
with open(options.c2bdg) as f: pass
if not options.peaks1 == '':
info("Read peaks for condition 1...")
p1io = PeakIO()
with open(options.peaks1, 'rU') as f:
p1io.read_from_xls(f)
if not options.peaks2 == '':
info("Read peaks for condition 2...")
p2io = PeakIO()
with open(options.peaks2, 'rU') as f:
p2io.read_from_xls(f)
#1 Read tag files
info("Read and build treatment 1 bedGraph...")
t1bio = cBedGraphIO.bedGraphIO(options.t1bdg)
t1btrack = t1bio.build_bdgtrack()
info("Read and build control 1 bedGraph...")
c1bio = cBedGraphIO.bedGraphIO(options.c1bdg)
c1btrack = c1bio.build_bdgtrack()
if len(options.depth) >=2:
depth1 = options.depth[0]
depth2 = options.depth[1]
else:
depth1 = options.depth[0]
depth2 = depth1
info("Read and build treatment 2 bedGraph...")
t2bio = cBedGraphIO.bedGraphIO(options.t2bdg)
t2btrack = t2bio.build_bdgtrack()
info("Read and build control 2 bedGraph...")
c2bio = cBedGraphIO.bedGraphIO(options.c2bdg)
c2btrack = c2bio.build_bdgtrack()
#3 Call Peaks
diffscore = DiffScoreTrackI( t1btrack,
c1btrack,
t2btrack,
c2btrack,
depth1, depth2 )
diffscore.finalize()
if options.call_peaks:
diffscore.set_track_score_method(options.track_score_method)
info("Calling peaks")
if options.track_score_method == 'p':
diffscore.call_peaks(cutoff = options.peaks_log_pvalue,
min_length = options.pminlen)
elif options.track_score_method == 'q':
diffscore.call_peaks(cutoff = options.peaks_log_qvalue,
min_length = options.pminlen)
else:
raise NotImplementedError
else:
info("Using existing peaks")
diffscore.store_peaks(p1io, p2io)
info("Rebuilding chromosomes")
diffscore.rebuild_chromosomes()
diffscore.annotate_peaks()
info("Calling differentially occupied peaks")
if options.score_method == 'p':
diffscore.call_diff_peaks(cutoff = options.log_pvalue,
min_length = options.dminlen,
score_method = options.score_method)
if options.score_method == 'q':
diffscore.call_diff_peaks(cutoff = options.log_qvalue,
min_length = options.dminlen,
score_method = options.score_method)
# diffscore.print_some_peaks()
# diffscore.print_diff_peaks()
info("Write output xls and BED files...")
ofhd_xls = open( os.path.join( options.outdir, options.peakxls), "w" )
ofhd_xls.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls.write( options.argtxt+"\n" )
ofhd_bed = open( os.path.join( options.outdir, options.peakbed), "w" )
# pass write method so we can print too, and include name
diffscore.write_peaks(xls=ofhd_xls, bed=ofhd_bed,
name = options.name, name_prefix="%s_peak_",
description="Peaks for %s (Made with MACS v2, " + strftime("%x") + ")",
trackline=options.trackline)
ofhd_xls.close()
ofhd_bed.close()
if diffscore.has_peakio():
info("Write annotated peak xls files...")
ofhd_xls1 = open( os.path.join( options.outdir, options.peak1xls), "w" )
ofhd_xls1.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls1.write(options.argtxt+"\n")
ofhd_xls2 = open( os.path.join( options.outdir, options.peak2xls), "w" )
ofhd_xls2.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
ofhd_xls2.write(options.argtxt+"\n")
diffscore.write_peaks_by_summit(ofhd_xls1, ofhd_xls2,
name = options.name, name_prefix="%s_peak_")
ofhd_xls1.close()
ofhd_xls2.close()
if options.store_bdg:
info("#4 Write output bedgraph files...")
ofhd_logLR = open( os.path.join( options.outdir, options.bdglogLR), "w" )
ofhd_pvalue = open( os.path.join( options.outdir, options.bdgpvalue), "w" )
ofhd_logFC = open( os.path.join( options.outdir, options.bdglogFC), "w" )
diffscore.write_bedgraphs(logLR=ofhd_logLR, pvalue=ofhd_pvalue,
logFC=ofhd_logFC, name = options.name,
description=" for %s (Made with MACS v2, " + strftime("%x") + ")",
trackline=options.trackline)
ofhd_logLR.close()
ofhd_pvalue.close()
ofhd_logFC.close()
