def main(args):
inf1 = None
if re.search('\.gz$', args.depth_bed):
inf1 = gzip.open(args.depth_bed)
else:
inf1 = open(args.depth_bed)
inf2 = None
if re.search('\.gz$', args.feature_bed):
inf2 = gzip.open(args.feature_bed)
else:
inf2 = open(args.feature_bed)
of = sys.stdout
if args.output:
if re.search('\.gz$', args.output):
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
bs1 = BedStream(inf1)
bs2 = BedStream(inf2)
mls = MultiLocusStream([bs1, bs2])
for overlapped in mls:
[b1s, b2s] = overlapped.get_payload()
if len(b1s) == 0 or len(b2s) == 0: continue
for b1 in b1s:
m = union_range_array(b1, b2s, is_sorted=True)
for rng in m:
of.write("\t".join([str(x) for x in rng.get_bed_array()]) +
"\t" + b1.get_payload() + "\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input',help="Use - for STDIN")
parser.add_argument('-o','--output',help="output file or use STDOUT if not set")
args = parser.parse_args()
if args.input == '-':
args.input = sys.stdin
else: args.input = open(args.input)
gs = GPDStream(args.input)
ls = LocusStream(gs)
of = sys.stdout
if args.output:
if re.search('\.gz$',args.output):
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
for rng in ls:
sys.stderr.write(rng.get_range_string()+" \r")
gpds = rng.get_payload()
exs = []
for ex_set in [[y.get_range() for y in x.exons] for x in gpds]:
exs += ex_set
cov = ranges_to_coverage(exs)
#use our coverage data on each gpd entry now
for gpd in gpds:
totcov = 0
for exon in [x.get_range() for x in gpd.exons]:
gcovs = union_range_array(exon,cov,payload=2)
totcov += sum([x.get_payload()*x.length() for x in gcovs])
of.write(gpd.get_gene_name()+"\t"+str(gpd.get_exon_count())+"\t"+str(gpd.get_length())+"\t"+str(float(totcov)/float(gpd.get_length()))+"\n")
sys.stderr.write("\n")
of.close()
def main():
parser = argparse.ArgumentParser(
description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input', help="Use - for STDIN")
parser.add_argument('-o',
'--output',
help="output file or use STDOUT if not set")
args = parser.parse_args()
if args.input == '-':
args.input = sys.stdin
else:
args.input = open(args.input)
gs = GPDStream(args.input)
ls = LocusStream(gs)
of = sys.stdout
if args.output:
if re.search('\.gz$', args.output):
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
for rng in ls:
sys.stderr.write(rng.get_range_string() + " \r")
gpds = rng.get_payload()
exs = []
for ex_set in [[y.get_range() for y in x.exons] for x in gpds]:
exs += ex_set
cov = ranges_to_coverage(exs)
#use our coverage data on each gpd entry now
for gpd in gpds:
totcov = 0
for exon in [x.get_range() for x in gpd.exons]:
gcovs = union_range_array(exon, cov, payload=2)
totcov += sum([x.get_payload() * x.length() for x in gcovs])
of.write(gpd.get_gene_name() + "\t" + str(gpd.get_exon_count()) +
"\t" + str(gpd.get_length()) + "\t" +
str(float(totcov) / float(gpd.get_length())) + "\n")
sys.stderr.write("\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="For every gpd entry (sorted) intersect it with bed depth (sorted)",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('gpd_input',help="GPD file")
parser.add_argument('bed_depth_input',help="GPD file")
parser.add_argument('-o','--output',help="output file")
args = parser.parse_args()
inf1 = None
if re.search('\.gz$',args.gpd_input):
inf1 = gzip.open(args.gpd_input)
else:
inf1 = open(args.gpd_input)
inf2 = None
if re.search('\.gz$',args.bed_depth_input):
inf2 = gzip.open(args.bed_depth_input)
else:
inf2 = open(args.bed_depth_input)
gs = GPDStream(inf1)
bs = BedStream(inf2)
of = sys.stdout
if args.output:
if re.search('\.gz$',args.output):
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
mls = MultiLocusStream([gs,bs])
z = 0
for ml in mls:
z += 1
#if z%1000 == 0:
sys.stderr.write(ml.get_range_string()+" \r")
[gpds,beds] = ml.get_payload()
if len(gpds) == 0:
continue
if len(beds)==0:
for gpd in gpds:
of.write(gpd.get_gene_name()+"\t"+gpd.get_transcript_name()+"\t"+str(gpd.get_exon_count())+"\t"+str(gpd.get_length())+"\t0\t0\t0"+"\n")
continue
#break beds up by depth
#depths = {}
#for bed in beds:
# d = int(bed.get_payload())
# if d not in depths: depths[d] = []
# depths[d].append(bed)
#for gpd in gpds:
# clen = 0
# tot = 0
# for d in depths:
# covs = []
# for ex in [x.get_range() for x in gpd.exons]:
# clen += sum([x.overlap_size(ex) for x in depths[d]])
# tot += clen*d
# of.write(gpd.get_gene_name()+"\t"+gpd.get_transcript_name()+"\t"+str(gpd.get_exon_count())+"\t"+str(gpd.get_length())+"\t"+str(clen)+"\t"+str(float(clen)/float(gpd.get_length()))+"\t"+str(float(tot)/float(gpd.get_length()))+"\n")
for gpd in gpds:
covs = []
for ex in [x.get_range() for x in gpd.exons]:
c = union_range_array(ex,beds,payload=2)
covs += c
clen = sum([x.length() for x in covs if int(x.get_payload())>0])
tot = sum([x.length()*int(x.get_payload()) for x in covs])
of.write(gpd.get_gene_name()+"\t"+gpd.get_transcript_name()+"\t"+str(gpd.get_exon_count())+"\t"+str(gpd.get_length())+"\t"+str(clen)+"\t"+str(float(clen)/float(gpd.get_length()))+"\t"+str(float(tot)/float(gpd.get_length()))+"\n")
sys.stderr.write("\n")
of.close()
inf1.close()
inf2.close()
