def run( options ):
options = opt_validate( options )
scaling_factor = options.sfactor
pseudo_depth = 1.0/scaling_factor # not an actual depth, but its reciprocal, a trick to override SPMR while necessary.
info("Read and build treatment bedGraph...")
tbio = BedGraphIO.bedGraphIO(options.tfile)
tbtrack = tbio.build_bdgtrack()
info("Read and build control bedGraph...")
cbio = BedGraphIO.bedGraphIO(options.cfile)
cbtrack = cbio.build_bdgtrack()
info("Build scoreTrackII...")
sbtrack = tbtrack.make_scoreTrackII_for_macs( cbtrack, depth1 = pseudo_depth, depth2 = pseudo_depth )
if abs(scaling_factor-1) > 1e-6:
# Only for the case while your input is SPMR from MACS2 callpeak; Let's override SPMR.
info("Values in your input bedGraph files will be multiplied by %f ..." % scaling_factor)
sbtrack.change_normalization_method( ord('M') ) # a hack to override SPMR
sbtrack.set_pseudocount( options.pseudocount )
already_processed_method_list = []
for (i, method) in enumerate(options.method):
if method in already_processed_method_list:
continue
else:
already_processed_method_list.append( method )
info("Calculate scores comparing treatment and control by '%s'..." % method)
if options.ofile:
ofile = os.path.join( options.outdir, options.ofile[ i ] )
else:
ofile = os.path.join( options.outdir, options.oprefix + "_" + method + ".bdg" )
# build score track
if method == 'ppois':
sbtrack.change_score_method( ord('p') )
elif method == 'qpois':
sbtrack.change_score_method( ord('q') )
elif method == 'subtract':
sbtrack.change_score_method( ord('d') )
elif method == 'logFE':
sbtrack.change_score_method( ord('f') )
elif method == 'FE':
sbtrack.change_score_method( ord('F') )
elif method == 'logLR': # log likelihood
sbtrack.change_score_method( ord('l') )
elif method == 'slogLR': # log likelihood
sbtrack.change_score_method( ord('s') )
elif method == 'max':
sbtrack.change_score_method( ord('M') )
else:
raise Exception("Can't reach here!")
info("Write bedGraph of scores...")
ofhd = open(ofile,"wb")
sbtrack.write_bedGraph(ofhd,name="%s_Scores" % (method.upper()),description="Scores calculated by %s" % (method.upper()), column = 3)
info("Finished '%s'! Please check '%s'!" % (method, ofile))
def run( options ):
options = opt_validate( options )
scaling_factor = options.sfactor
pseudo_depth = 1.0/scaling_factor # not an actual depth, but its reciprocal, a trick to override SPMR while necessary.
info("Read and build treatment bedGraph...")
tbio = BedGraphIO.bedGraphIO(options.tfile)
tbtrack = tbio.build_bdgtrack()
info("Read and build control bedGraph...")
cbio = BedGraphIO.bedGraphIO(options.cfile)
cbtrack = cbio.build_bdgtrack()
info("Build scoreTrackII...")
sbtrack = tbtrack.make_scoreTrackII_for_macs( cbtrack, depth1 = pseudo_depth, depth2 = pseudo_depth )
if abs(scaling_factor-1) > 1e-6:
# Only for the case while your input is SPMR from MACS2 callpeak; Let's override SPMR.
info("Values in your input bedGraph files will be multiplied by %f ..." % scaling_factor)
sbtrack.change_normalization_method( ord('M') ) # a hack to override SPMR
sbtrack.set_pseudocount( options.pseudocount )
already_processed_method_list = []
for (i, method) in enumerate(options.method):
if method in already_processed_method_list:
continue
else:
already_processed_method_list.append( method )
info("Calculate scores comparing treatment and control by '%s'..." % method)
if options.ofile:
ofile = os.path.join( options.outdir, options.ofile[ i ] )
else:
ofile = os.path.join( options.outdir, options.oprefix + "_" + method + ".bdg" )
# build score track
if method == 'ppois':
sbtrack.change_score_method( ord('p') )
elif method == 'qpois':
sbtrack.change_score_method( ord('q') )
elif method == 'subtract':
sbtrack.change_score_method( ord('d') )
elif method == 'logFE':
sbtrack.change_score_method( ord('f') )
elif method == 'FE':
sbtrack.change_score_method( ord('F') )
elif method == 'logLR': # log likelihood
sbtrack.change_score_method( ord('l') )
elif method == 'slogLR': # log likelihood
sbtrack.change_score_method( ord('s') )
elif method == 'max':
sbtrack.change_score_method( ord('M') )
else:
raise Exception("Can't reach here!")
info("Write bedGraph of scores...")
ofhd = open(ofile,"w")
sbtrack.write_bedGraph(ofhd,name="%s_Scores" % (method.upper()),description="Scores calculated by %s" % (method.upper()), column = 3)
info("Finished '%s'! Please check '%s'!" % (method, ofile))
def run(options):
info("Read and build bedGraph...")
bio = BedGraphIO.bedGraphIO(options.ifile)
btrack = bio.build_bdgtrack(baseline_value=0)
info("Call peaks from bedGraph...")
#(peaks,bpeaks) = btrack.call_broadpeaks (lvl1_cutoff=options.cutoffpeak, lvl2_cutoff=options.cutofflink, min_length=options.minlen, lvl1_max_gap=options.lvl1maxgap, lvl2_max_gap=options.lvl2maxgap)
bpeaks = btrack.call_broadpeaks(lvl1_cutoff=options.cutoffpeak,
lvl2_cutoff=options.cutofflink,
min_length=options.minlen,
lvl1_max_gap=options.lvl1maxgap,
lvl2_max_gap=options.lvl2maxgap)
info("Write peaks...")
#nf = open ("%s_c%.1f_l%d_g%d_peaks.encodePeak" % (options.oprefix,options.cutoffpeak,options.minlen,options.lvl1maxgap),"w")
if options.ofile:
bf = open(os.path.join(options.outdir, options.ofile), "w")
options.oprefix = options.ofile
else:
bf = open(
os.path.join(
options.outdir, "%s_c%.1f_C%.2f_l%d_g%d_G%d_broad.bed12" %
(options.oprefix, options.cutoffpeak, options.cutofflink,
options.minlen, options.lvl1maxgap, options.lvl2maxgap)), "w")
bpeaks[1].write_to_gappedPeak(bf,
name_prefix=options.oprefix + "_broadRegion")
info("Done")
def run( options ):
options = opt_validate( options )
info("Read and build bedGraph...")
bio = BedGraphIO.bedGraphIO(options.ifile)
btrack = bio.build_bdgtrack(baseline_value=0)
info("Modify bedGraph...")
if options.method.lower() == "p2q":
btrack.p2q()
else:
extraparam = float(options.extraparam[0])
if options.method.lower() == "multiply":
btrack.apply_func( lambda x: x * extraparam)
elif options.method.lower() == "add":
btrack.apply_func( lambda x: x + extraparam)
elif options.method.lower() == "max":
btrack.apply_func( lambda x: x if x> extraparam else extraparam )
elif options.method.lower() == "min":
btrack.apply_func( lambda x: x if x< extraparam else extraparam )
ofile = os.path.join( options.outdir, options.ofile )
info("Write bedGraph of modified scores...")
ofhd = open(ofile,"w")
btrack.write_bedGraph(ofhd,name="%s_modified_scores" % (options.method.upper()),description="Scores calculated by %s" % (options.method.upper()))
info("Finished '%s'! Please check '%s'!" % (options.method, ofile))
def run( options ):
options = opt_validate( options )
info("Read and build bedGraph...")
bio = BedGraphIO.bedGraphIO(options.ifile)
btrack = bio.build_bdgtrack(baseline_value=0)
info("Modify bedGraph...")
if options.method.lower() == "p2q":
btrack.p2q()
elif options.method.lower() == "analen":
btrack.analen()
else:
extraparam = float(options.extraparam[0])
if options.method.lower() == "multiply":
btrack.apply_func( lambda x: x * extraparam)
elif options.method.lower() == "add":
btrack.apply_func( lambda x: x + extraparam)
elif options.method.lower() == "max":
btrack.apply_func( lambda x: x if x> extraparam else extraparam )
elif options.method.lower() == "min":
btrack.apply_func( lambda x: x if x< extraparam else extraparam )
ofile = os.path.join( options.outdir, options.ofile )
info("Write bedGraph of modified scores...")
ofhd = open(ofile,"wb")
btrack.write_bedGraph(ofhd,name="%s_modified_scores" % (options.method.upper()),description="Scores calculated by %s" % (options.method.upper()))
info("Finished '%s'! Please check '%s'!" % (options.method, ofile))
def run(options):
options = opt_validate(options)
#weights = options.weights
info("Read and build bedGraph for each replicate...")
reps = []
i = 1
for ifile in options.ifile:
info("Read file #%d" % i)
reps.append(BedGraphIO.bedGraphIO(ifile).build_bdgtrack())
i += 1
# first two reps
info("combining tracks 1-%i with method '%s'" % (i - 1, options.method))
cmbtrack = reps[0].overlie([reps[j] for j in range(1, i - 1)],
func=options.method)
ofile = os.path.join(options.outdir, options.ofile)
info("Write bedGraph of combined scores...")
ofhd = open(ofile, "w")
cmbtrack.write_bedGraph(
ofhd,
name="%s_combined_scores" % (options.method.upper()),
description="Scores calculated by %s" % (options.method.upper()))
info("Finished '%s'! Please check '%s'!" % (options.method, ofile))
def run( options ):
info("Read and build bedGraph...")
bio = BedGraphIO.bedGraphIO(options.ifile)
btrack = bio.build_bdgtrack(baseline_value=0)
if options.cutoff_analysis:
info("Analyze cutoff vs number of peaks/total length of peaks/average length of peak")
cutoff_analysis_result = btrack.cutoff_analysis( int(options.maxgap), int(options.minlen), 50 )
info("Write report...")
if options.ofile:
fhd = open( os.path.join( options.outdir, options.ofile ), 'w' )
else:
fhd = open ( os.path.join( options.outdir, "%s_l%d_g%d_cutoff_analysis.txt" % (options.oprefix,options.minlen,options.maxgap)), "w" )
fhd.write( cutoff_analysis_result )
info("Done")
else:
info("Call peaks from bedGraph...")
peaks = btrack.call_peaks(cutoff=float(options.cutoff),min_length=int(options.minlen),max_gap=int(options.maxgap),call_summits=options.call_summits)
info("Write peaks...")
if options.ofile:
options.oprefix = options.ofile
nf = open( os.path.join( options.outdir, options.ofile ), 'w' )
else:
nf = open ( os.path.join( options.outdir, "%s_c%.1f_l%d_g%d_peaks.narrowPeak" % (options.oprefix,options.cutoff,options.minlen,options.maxgap)), "w" )
peaks.write_to_narrowPeak(nf, name=options.oprefix, name_prefix=options.oprefix+"_narrowPeak", score_column="score", trackline=options.trackline)
info("Done")
def run( options ):
info("Read and build bedGraph...")
bio = BedGraphIO.bedGraphIO(options.ifile)
btrack = bio.build_bdgtrack(baseline_value=0)
info("Call peaks from bedGraph...")
#(peaks,bpeaks) = btrack.call_broadpeaks (lvl1_cutoff=options.cutoffpeak, lvl2_cutoff=options.cutofflink, min_length=options.minlen, lvl1_max_gap=options.lvl1maxgap, lvl2_max_gap=options.lvl2maxgap)
bpeaks = btrack.call_broadpeaks (lvl1_cutoff=options.cutoffpeak, lvl2_cutoff=options.cutofflink, min_length=options.minlen, lvl1_max_gap=options.lvl1maxgap, lvl2_max_gap=options.lvl2maxgap)
info("Write peaks...")
#nf = open ("%s_c%.1f_l%d_g%d_peaks.encodePeak" % (options.oprefix,options.cutoffpeak,options.minlen,options.lvl1maxgap),"w")
if options.ofile:
bf = open( os.path.join( options.outdir, options.ofile ), "w" )
options.oprefix = options.ofile
else:
bf = open ( os.path.join( options.outdir, "%s_c%.1f_C%.2f_l%d_g%d_G%d_broad.bed12" % (options.oprefix,options.cutoffpeak,options.cutofflink,options.minlen,options.lvl1maxgap,options.lvl2maxgap)), "w" )
bpeaks[1].write_to_gappedPeak(bf, name_prefix=options.oprefix+"_broadRegion")
info("Done")
def run( options ):
options = opt_validate( options )
#weights = options.weights
info("Read and build bedGraph for each replicate...")
reps = []
i = 1
for ifile in options.ifile:
info("Read file #%d" % i)
reps.append( BedGraphIO.bedGraphIO( ifile ).build_bdgtrack( ) )
i += 1
# first two reps
info("combining #1 and #2 with method '%s'" % options.method)
cmbtrack = reps[ 0 ].overlie( reps[ 1 ], func=options.method )
ofile = os.path.join( options.outdir, options.ofile )
info("Write bedGraph of combined scores...")
ofhd = open(ofile,"wb")
cmbtrack.write_bedGraph(ofhd,name="%s_combined_scores" % (options.method.upper()),description="Scores calculated by %s" % (options.method.upper()))
info("Finished '%s'! Please check '%s'!" % (options.method, ofile))
def run(options):
if options.maxgap >= options.minlen:
error(
"MAXGAP should be smaller than MINLEN! Your input is MAXGAP = %d and MINLEN = %d"
% (options.maxgap, options.minlen))
LLR_cutoff = options.cutoff
ofile_prefix = options.oprefix
info("Read and build treatment 1 bedGraph...")
t1bio = BedGraphIO.bedGraphIO(options.t1bdg)
t1btrack = t1bio.build_bdgtrack()
info("Read and build control 1 bedGraph...")
c1bio = BedGraphIO.bedGraphIO(options.c1bdg)
c1btrack = c1bio.build_bdgtrack()
info("Read and build treatment 2 bedGraph...")
t2bio = BedGraphIO.bedGraphIO(options.t2bdg)
t2btrack = t2bio.build_bdgtrack()
info("Read and build control 2 bedGraph...")
c2bio = BedGraphIO.bedGraphIO(options.c2bdg)
c2btrack = c2bio.build_bdgtrack()
depth1 = options.depth1
depth2 = options.depth2
if depth1 > depth2: # scale down condition 1 to size of condition 2
depth1 = depth2 / depth1
depth2 = 1.0
elif depth1 < depth2: # scale down condition 2 to size of condition 1
depth2 = depth1 / depth2
depth1 = 1.0
else: # no need to scale down any
depth1 = 1.0
depth2 = 1.0
twoconditionscore = ScoreTrack.TwoConditionScores(t1btrack, c1btrack,
t2btrack, c2btrack,
depth1, depth2)
twoconditionscore.build()
twoconditionscore.finalize()
(cat1, cat2,
cat3) = twoconditionscore.call_peaks(min_length=options.minlen,
max_gap=options.maxgap,
cutoff=options.cutoff)
info("Write peaks...")
ofiles = []
name_prefix = []
if options.ofile:
ofiles = map(lambda x: os.path.join(options.outdir, x), options.ofile)
name_prefix = options.ofile
else:
ofiles = [
os.path.join(
options.outdir,
"%s_c%.1f_cond1.bed" % (options.oprefix, options.cutoff)),
os.path.join(
options.outdir,
"%s_c%.1f_cond2.bed" % (options.oprefix, options.cutoff)),
os.path.join(
options.outdir,
"%s_c%.1f_common.bed" % (options.oprefix, options.cutoff))
]
name_prefix = [
options.oprefix + "_cond1_",
options.oprefix + "_cond2_",
options.oprefix + "_common_",
]
nf = open(ofiles[0], 'w')
cat1.write_to_bed(nf,
name_prefix=name_prefix[0],
name="condition 1",
description="unique regions in condition 1",
score_column="score")
nf = open(ofiles[1], 'w')
cat2.write_to_bed(nf,
name_prefix=name_prefix[1],
name="condition 2",
description="unique regions in condition 2",
score_column="score")
nf = open(ofiles[2], 'w')
cat3.write_to_bed(nf,
name_prefix=name_prefix[2],
name="common",
description="common regions in both conditions",
score_column="score")
info("Done")
def run( options ):
if options.maxgap >= options.minlen:
error("MAXGAP should be smaller than MINLEN! Your input is MAXGAP = %d and MINLEN = %d" % (options.maxgap, options.minlen))
LLR_cutoff = options.cutoff
ofile_prefix = options.oprefix
info("Read and build treatment 1 bedGraph...")
t1bio = BedGraphIO.bedGraphIO(options.t1bdg)
t1btrack = t1bio.build_bdgtrack()
info("Read and build control 1 bedGraph...")
c1bio = BedGraphIO.bedGraphIO(options.c1bdg)
c1btrack = c1bio.build_bdgtrack()
info("Read and build treatment 2 bedGraph...")
t2bio = BedGraphIO.bedGraphIO(options.t2bdg)
t2btrack = t2bio.build_bdgtrack()
info("Read and build control 2 bedGraph...")
c2bio = BedGraphIO.bedGraphIO(options.c2bdg)
c2btrack = c2bio.build_bdgtrack()
depth1 = options.depth1
depth2 = options.depth2
if depth1 > depth2: # scale down condition 1 to size of condition 2
depth1 = depth2 / depth1
depth2 = 1.0
elif depth1 < depth2: # scale down condition 2 to size of condition 1
depth2 = depth1/ depth2
depth1 = 1.0
else: # no need to scale down any
depth1 = 1.0
depth2 = 1.0
twoconditionscore = ScoreTrack.TwoConditionScores( t1btrack,
c1btrack,
t2btrack,
c2btrack,
depth1,
depth2 )
twoconditionscore.build()
twoconditionscore.finalize()
(cat1,cat2,cat3) = twoconditionscore.call_peaks(min_length=options.minlen, max_gap=options.maxgap, cutoff=options.cutoff)
info("Write peaks...")
ofiles = []
name_prefix = []
if options.ofile:
ofiles = map( lambda x: os.path.join( options.outdir, x ), options.ofile )
name_prefix = options.ofile
else:
ofiles = [ os.path.join( options.outdir, "%s_c%.1f_cond1.bed" % (options.oprefix,options.cutoff)),
os.path.join( options.outdir, "%s_c%.1f_cond2.bed" % (options.oprefix,options.cutoff)),
os.path.join( options.outdir, "%s_c%.1f_common.bed" % (options.oprefix,options.cutoff))
]
name_prefix = [ options.oprefix+"_cond1_",
options.oprefix+"_cond2_",
options.oprefix+"_common_",
]
nf = open( ofiles[ 0 ], 'w' )
cat1.write_to_bed(nf, name_prefix=name_prefix[ 0 ], name="condition 1", description="unique regions in condition 1", score_column="score")
nf = open( ofiles[ 1 ], 'w' )
cat2.write_to_bed(nf, name_prefix=name_prefix[ 1 ], name="condition 2", description="unique regions in condition 2", score_column="score")
nf = open( ofiles[ 2 ], 'w' )
cat3.write_to_bed(nf, name_prefix=name_prefix[ 2 ], name="common", description="common regions in both conditions", score_column="score")
info("Done")
