def get_output(bedarray,z):
sarray = sort_genomic_ranges(bedarray[:])
covs = ranges_to_coverage(bedarray)
olines = ''
for c in covs:
olines += c.chr+"\t"+str(c.start-1)+"\t"+str(c.end)+"\t"+str(c.get_payload())+"\n"
return [olines,z]
def main(args):
inf = sys.stdin
if args.input != '-':
if re.search('\.gz$', args.input):
inf = gzip.open(args.input)
else:
inf = open(args.input)
of = sys.stdout
if args.output:
if re.search('\.gz$', args.output):
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
loci = LocusStream(GPDStream(inf))
for locus in loci:
exranges = []
for entry in locus.get_payload():
for exon in entry.exons:
exranges.append(exon.get_range())
covs = ranges_to_coverage(exranges)
for cov in covs:
of.write("\t".join([str(x) for x in cov.get_bed_coordinates()]) +
"\t" + str(+cov.get_payload()) + "\n")
of.close()
inf.close()
def get_depth_per_transcript(self,mindepth=1):
bedarray = []
for tx in self.get_transcripts():
for ex in [x.rng for x in tx.exons]: bedarray.append(ex)
cov = ranges_to_coverage(bedarray)
results = {}
for tx in self.get_transcripts():
tlen = tx.get_length()
bcov = []
for ex in [x.rng for x in tx.exons]:
excov = [[x.overlap_size(ex),x.get_payload()] for x in cov]
for coved in [x for x in excov if x[0] > 0]:
bcov.append(coved)
total_base_coverage = sum([x[0]*x[1] for x in bcov])
average_coverage = float(total_base_coverage)/float(tlen)
minimum_bases_covered = sum([x[0] for x in bcov if x[1] >= mindepth])
fraction_covered_at_minimum = float(minimum_bases_covered)/float(tlen)
res = {'tx':tx,'average_coverage':average_coverage,'fraction_covered':fraction_covered_at_minimum,'mindepth':mindepth,'length_covered':minimum_bases_covered}
results[tx.get_id()] = res
#print average_coverage
#print fraction_covered_at_minimum
#print tlen
#tcov = float(bcov)/float(tlen)
#print tcov
#for c in cov:
# print c
return results
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 do_tx_line(ref_gpd, annots, reads, args):
allbits = []
read_count = 0
for read in reads:
if not args.allow_overflowed_matches and read.get_range(
).start < ref_gpd.get_range().start:
continue
if not args.allow_overflowed_matches and read.get_range(
).end > ref_gpd.get_range().end:
continue
v = ref_gpd.union(read)
for e in [x.rng for x in v.exons]:
allbits.append(e)
read_count += 1
if len(allbits) == 0: return None
if read_count < args.minimum_read_count: return None
cov = ranges_to_coverage(allbits)
#print [x.get_payload() for x in cov]
curr = 0
bps = []
for i in range(0, ref_gpd.get_length()):
bps.append(0)
for rng1 in [x.rng for x in ref_gpd.exons]:
overs = [[z[0], z[1].get_payload()]
for z in [[y.union(rng1), y] for y in cov] if z[0]]
for ov in overs:
dist1 = ov[0].start - rng1.start + curr
dist2 = ov[0].end - rng1.start + curr
for i in range(dist1, dist2 + 1):
bps[i] += ov[1]
curr += rng1.length()
trimmedbps = bps
if args.only_covered_ends:
start = 0
finish = len(bps) - 1
for i in range(0, len(bps)):
if bps[i] != 0:
start = i
break
for i in reversed(range(0, len(bps))):
if bps[i] != 0:
finish = i
break
trimmedbps = bps[start:finish + 1]
exp = float(sum(trimmedbps)) / float(len(trimmedbps))
if ref_gpd.get_strand() == '-': trimmedbps = list(reversed(trimmedbps))
if len(trimmedbps) < args.minimum_read_count: return None
#bin the results
vals = {}
for dat in [[
str(1 + int(100 * float(i) / float(len(trimmedbps)))),
float(trimmedbps[i]) / float(read_count)
] for i in range(0, len(trimmedbps))]:
if dat[0] not in vals: vals[dat[0]] = []
vals[dat[0]].append(dat[1])
for num in vals:
vals[num] = average(vals[num])
return [vals, read_count, exp, len(trimmedbps), ref_gpd.get_exon_count()]
def main():
parser = argparse.ArgumentParser(
description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input', help="IDP output folder")
#parser.add_argument('--min_exons',type=int,default=1,help="At least this number of exons")
parser.add_argument('--offset',
type=int,
default=1,
help="add this much to all expressions")
parser.add_argument('--mult',
type=int,
default=10,
help="multiply all expressions by this much")
parser.add_argument('-o',
'--output',
help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
args.input = args.input.rstrip('/')
inf = open(args.input + '/isoform.gpd')
sys.stderr.write("Reading isoform.gpd\n")
txs = {}
for line in inf:
gpd = GPD(line)
tx = gpd.get_transcript_name()
if tx not in txs:
txs[tx] = []
for exon in gpd.exons:
txs[tx].append(exon.get_range())
inf.close()
sys.stderr.write("Reading isoform.exp file\n")
inf = open(args.input + '/isoform.exp')
vals = []
for line in inf:
f = line.rstrip().split("\t")
v = int((float(f[1]) * args.mult) + args.offset)
tx = f[0]
exons = txs[tx]
#if len(exons) < args.min_exons: continue
for i in range(0, v):
vals += exons[:]
inf.close()
sys.stderr.write("Generating coverage file " + str(len(vals)) + "\n")
of = sys.stdout
if args.output:
if args.output[-3:] == '.gz':
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr + "\t" + str(v.start - 1) + "\t" + str(v.end) + "\t" +
str(v.get_payload()) + "\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input',help="Use - for STDIN")
parser.add_argument('--offset',type=int,default=0,help="add this much to transcript tpms")
parser.add_argument('--mult',type=int,default=10,help="multiply this much to tpms")
parser.add_argument('--min_exons',type=int,default=1,help="require at least this many exons")
parser.add_argument('-o','--output',help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
inf = sys.stdin
if args.input != '-':
if args.input[-3:]=='.gz':
inf = gzip.open(args.input)
else: inf = open(args.input)
genes = {}
sys.stderr.write("Reading gtf file\n")
txs = {}
for line in inf:
if re.match('#',line): continue
f = line.rstrip().split("\t")
tx = None
if f[2] == 'exon' or f[2] == 'transcript':
tx = re.search('transcript_id\s+"([^"]+)"',f[8]).group(1)
if tx not in txs:
txs[tx] = {}
txs[tx]['tpm'] = 0
txs[tx]['exons'] = []
if f[2] == 'transcript':
tpm = float(re.search('TPM\s+"([^"]+)"',f[8]).group(1))
txs[tx]['tpm'] = int((tpm*float(args.mult))+args.offset)
if f[2] == 'exon':
chr = f[0]
start = int(f[3])-1
end = int(f[4])
txs[tx]['exons'].append(Bed(chr,start,end))
inf.close()
vals = []
sys.stderr.write("Traversing annotation file\n")
for tx in txs:
exons = txs[tx]['exons']
v = txs[tx]['tpm']
if len(exons) < args.min_exons: continue
for i in range(0,v):
vals += exons[:]
sys.stderr.write("Generating coverage file "+str(len(vals))+"\n")
of = sys.stdout
if args.output:
if args.output[-3:]=='.gz':
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr+"\t"+str(v.start-1)+"\t"+str(v.end)+"\t"+str(v.get_payload())+"\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\n")
of.close()
def do_locus(locus):
exranges = []
for entry in locus.get_payload():
for exon in entry.exons:
exranges.append(exon.get_range())
covs = ranges_to_coverage(exranges)
output = []
for cov in covs:
output.append("\t".join([str(x) for x in cov.get_bed_coordinates()])+"\t"+str(+cov.get_payload())+"\n")
return output
def do_locus(locus):
exranges = []
for entry in locus.get_payload():
for exon in entry.exons:
exranges.append(exon.get_range())
covs = ranges_to_coverage(exranges)
output = []
for cov in covs:
output.append("\t".join([str(x) for x in cov.get_bed_coordinates()]) +
"\t" + str(+cov.get_payload()) + "\n")
return output
def main():
parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input',help="IDP output folder")
#parser.add_argument('--min_exons',type=int,default=1,help="At least this number of exons")
parser.add_argument('--offset',type=int,default=1,help="add this much to all expressions")
parser.add_argument('--mult',type=int,default=10,help="multiply all expressions by this much")
parser.add_argument('-o','--output',help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
args.input= args.input.rstrip('/')
inf = open(args.input+'/isoform.gpd')
sys.stderr.write("Reading isoform.gpd\n")
txs = {}
for line in inf:
gpd = GPD(line)
tx = gpd.get_transcript_name()
if tx not in txs:
txs[tx] = []
for exon in gpd.exons:
txs[tx].append(exon.get_range())
inf.close()
sys.stderr.write("Reading isoform.exp file\n")
inf = open(args.input+'/isoform.exp')
vals = []
for line in inf:
f = line.rstrip().split("\t")
v = int((float(f[1])*args.mult)+args.offset)
tx = f[0]
exons = txs[tx]
#if len(exons) < args.min_exons: continue
for i in range(0,v):
vals += exons[:]
inf.close()
sys.stderr.write("Generating coverage file "+str(len(vals))+"\n")
of = sys.stdout
if args.output:
if args.output[-3:]=='.gz':
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr+"\t"+str(v.start-1)+"\t"+str(v.end)+"\t"+str(v.get_payload())+"\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\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 get_depth_per_transcript(self, mindepth=1):
bedarray = []
for tx in self.get_transcripts():
for ex in [x.rng for x in tx.exons]:
bedarray.append(ex)
cov = ranges_to_coverage(bedarray)
results = {}
for tx in self.get_transcripts():
tlen = tx.get_length()
bcov = []
for ex in [x.rng for x in tx.exons]:
excov = [[x.overlap_size(ex), x.get_payload()] for x in cov]
for coved in [x for x in excov if x[0] > 0]:
bcov.append(coved)
total_base_coverage = sum([x[0] * x[1] for x in bcov])
average_coverage = float(total_base_coverage) / float(tlen)
minimum_bases_covered = sum(
[x[0] for x in bcov if x[1] >= mindepth])
fraction_covered_at_minimum = float(minimum_bases_covered) / float(
tlen)
res = {
'tx': tx,
'average_coverage': average_coverage,
'fraction_covered': fraction_covered_at_minimum,
'mindepth': mindepth,
'length_covered': minimum_bases_covered
}
results[tx.get_id()] = res
#print average_coverage
#print fraction_covered_at_minimum
#print tlen
#tcov = float(bcov)/float(tlen)
#print tcov
#for c in cov:
# print c
return results
def main():
parser = argparse.ArgumentParser(
description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input', help="Use - for STDIN")
parser.add_argument('genepred', help="the genepred used for this alignqc")
parser.add_argument('--min_exons',
type=int,
default=1,
help="At least this number of exons")
parser.add_argument('--full',
action='store_true',
help="only use full matches")
parser.add_argument('-o',
'--output',
help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
inf = sys.stdin
if args.input != '-':
if args.input[-3:] == '.gz':
inf = gzip.open(args.input)
else:
inf = open(args.input)
genes = {}
sys.stderr.write("Reading annotation file\n")
for line in inf:
f = line.rstrip().split("\t")
gene = f[2]
tx = f[3]
type = f[4]
if args.full and type != 'full': continue
if gene not in genes:
genes[gene] = {}
genes[gene]['transcripts'] = {}
genes[gene]['cnt'] = 0
if tx not in genes[gene]['transcripts']:
genes[gene]['transcripts'][tx] = 0
genes[gene]['cnt'] += 1
genes[gene]['transcripts'][tx] += 1
inf.close()
txs = {}
sys.stderr.write("Reading genepred file\n")
z = 0
with open(args.genepred) as inf:
for line in inf:
z += 1
if z % 1000 == 0: sys.stderr.write(str(z) + " \r")
gpd = GPD(line)
exs = []
for ex in gpd.exons:
exs.append(ex.get_range())
txs[gpd.get_transcript_name()] = exs
sys.stderr.write("\n")
vals = []
sys.stderr.write("Traversing annotation file\n")
for gene in genes:
for tx in genes[gene]['transcripts']:
v = genes[gene]['transcripts'][tx]
exons = txs[tx]
if len(exons) < args.min_exons: continue
for i in range(0, v):
vals += exons[:]
sys.stderr.write("Generating coverage file " + str(len(vals)) + "\n")
of = sys.stdout
if args.output:
if args.output[-3:] == '.gz':
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr + "\t" + str(v.start - 1) + "\t" + str(v.end) + "\t" +
str(v.get_payload()) + "\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\n")
of.close()
def main():
parser = argparse.ArgumentParser(
description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input', help="Use - for STDIN")
parser.add_argument('--offset',
type=int,
default=0,
help="add this much to transcript tpms")
parser.add_argument('--mult',
type=int,
default=10,
help="multiply this much to tpms")
parser.add_argument('--min_exons',
type=int,
default=1,
help="require at least this many exons")
parser.add_argument('-o',
'--output',
help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
inf = sys.stdin
if args.input != '-':
if args.input[-3:] == '.gz':
inf = gzip.open(args.input)
else:
inf = open(args.input)
genes = {}
sys.stderr.write("Reading gtf file\n")
txs = {}
for line in inf:
if re.match('#', line): continue
f = line.rstrip().split("\t")
tx = None
if f[2] == 'exon' or f[2] == 'transcript':
tx = re.search('transcript_id\s+"([^"]+)"', f[8]).group(1)
if tx not in txs:
txs[tx] = {}
txs[tx]['tpm'] = 0
txs[tx]['exons'] = []
if f[2] == 'transcript':
tpm = float(re.search('TPM\s+"([^"]+)"', f[8]).group(1))
txs[tx]['tpm'] = int((tpm * float(args.mult)) + args.offset)
if f[2] == 'exon':
chr = f[0]
start = int(f[3]) - 1
end = int(f[4])
txs[tx]['exons'].append(Bed(chr, start, end))
inf.close()
vals = []
sys.stderr.write("Traversing annotation file\n")
for tx in txs:
exons = txs[tx]['exons']
v = txs[tx]['tpm']
if len(exons) < args.min_exons: continue
for i in range(0, v):
vals += exons[:]
sys.stderr.write("Generating coverage file " + str(len(vals)) + "\n")
of = sys.stdout
if args.output:
if args.output[-3:] == '.gz':
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr + "\t" + str(v.start - 1) + "\t" + str(v.end) + "\t" +
str(v.get_payload()) + "\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\n")
of.close()
def main():
parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input',help="Use - for STDIN")
parser.add_argument('genepred',help="the genepred used for this alignqc")
parser.add_argument('--min_exons',type=int,default=1,help="At least this number of exons")
parser.add_argument('--full',action='store_true',help="only use full matches")
parser.add_argument('-o','--output',help="OUTPUT file or nothing for STDOUT")
args = parser.parse_args()
inf = sys.stdin
if args.input != '-':
if args.input[-3:]=='.gz':
inf = gzip.open(args.input)
else: inf = open(args.input)
genes = {}
sys.stderr.write("Reading annotation file\n")
for line in inf:
f = line.rstrip().split("\t")
gene = f[2]
tx = f[3]
type = f[4]
if args.full and type != 'full': continue
if gene not in genes:
genes[gene] = {}
genes[gene]['transcripts'] = {}
genes[gene]['cnt'] = 0
if tx not in genes[gene]['transcripts']:
genes[gene]['transcripts'][tx] = 0
genes[gene]['cnt'] += 1
genes[gene]['transcripts'][tx] += 1
inf.close()
txs = {}
sys.stderr.write("Reading genepred file\n")
z = 0
with open(args.genepred) as inf:
for line in inf:
z +=1
if z%1000==0: sys.stderr.write(str(z)+" \r")
gpd = GPD(line)
exs = []
for ex in gpd.exons:
exs.append(ex.range)
txs[gpd.get_transcript_name()] = exs
sys.stderr.write("\n")
vals = []
sys.stderr.write("Traversing annotation file\n")
for gene in genes:
for tx in genes[gene]['transcripts']:
v = genes[gene]['transcripts'][tx]
exons = txs[tx]
if len(exons) < args.min_exons: continue
for i in range(0,v):
vals += exons[:]
sys.stderr.write("Generating coverage file "+str(len(vals))+"\n")
of = sys.stdout
if args.output:
if args.output[-3:]=='.gz':
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
covs = ranges_to_coverage(vals)
for v in covs:
of.write(v.chr+"\t"+str(v.start-1)+"\t"+str(v.end)+"\t"+str(v.get_payload())+"\n")
# of.write(tx+"\t"+gene+"\t"+str(genes[gene]['transcripts'][tx])+"\t"+str(genes[gene]['cnt'])+"\n")
of.close()