def process_locus(locus, args):
depth = {}
s2psl = SAMtoPSLconversionFactory()
unique = {}
chr = locus[0].value('rname')
for sam in locus:
p = PSL(s2psl.convert_line(sam.get_line()))
g = GenePredEntry(p.get_genepred_line())
g = g.get_smoothed(args.min_intron)
for i in range(0,g.get_exon_count()):
rng = str(g.value('exonStarts')[i])+"\t"+str(g.value('exonEnds')[i])
if rng not in unique: unique[rng] = 0
unique[rng]+=1
for bstr in unique:
[start,end] = bstr.split("\t")
for i in range(int(start),int(end)):
if i not in depth: depth[i] = 0
depth[i] += unique[bstr] # add the number of these to the depth
#now we can print the depth
prevdepth = 0
prevstart = None
lasti = None
for i in sorted(depth.keys()):
if depth[i] < args.min_depth: continue
if depth[i] != prevdepth: #output what we have so far if we have something
if prevstart:
output_depth(chr+"\t"+str(prevstart)+"\t"+str(lasti+1)+"\t"+str(prevdepth),args)
prevstart = i
prevdepth = depth[i]
lasti = i
if prevstart:
output_depth(chr+"\t"+str(prevstart)+"\t"+str(lasti+1)+"\t"+str(prevdepth),args)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('gpd_input')
parser.add_argument('bam_input')
parser.add_argument('--intergenic_buffer',default=10000,type=int)
parser.add_argument('--window_size',default=10000,type=int)
parser.add_argument('--bin_size',default=1000,type=int)
parser.add_argument('--use_off_regions',action='store_true',help="Use a region even if there is no reads mapped to it.")
parser.add_argument('--get_exons',action='store_true')
args = parser.parse_args()
chr_beds = {}
gene_beds = []
exon_beds = []
sys.stderr.write("Reading genepred file\n")
asum = 0
atot = 0
with open(args.gpd_input) as inf:
for line in inf:
g = GenePredEntry(line)
asum += g.length()
atot += 1
grng = g.get_bed()
grng.direction = None
if grng.chr not in chr_beds:
chr_beds[grng.chr] = grng.copy()
chr_beds[grng.chr] = chr_beds[grng.chr].merge(grng)
gene_beds.append(grng)
for i in range(0,g.get_exon_count()):
erng = Bed(g.value('chrom'),g.value('exonStarts')[i],g.value('exonEnds')[i])
exon_beds.append(erng)
avglen = float(asum)/float(atot)
sys.stderr.write("Sorting gene bed\n")
gene_beds = sort_ranges(gene_beds)
gene_beds = merge_ranges(gene_beds,already_sorted=True)
sys.stderr.write("Sorting chromosome beds\n")
chr_beds = sort_ranges([chr_beds[x] for x in chr_beds.keys()])
sys.stderr.write("Sorting exon beds\n")
exon_beds = sort_ranges(exon_beds)
sys.stderr.write("Get padded genes\n")
padded_gene_beds = pad_ranges(gene_beds,args.intergenic_buffer,chr_beds)
padded_gene_beds = merge_ranges(padded_gene_beds,already_sorted=True)
sys.stderr.write("Get intergenic regions\n")
intergenic_beds = subtract_ranges(chr_beds,padded_gene_beds,already_sorted=True)
intergenic_beds = merge_ranges(intergenic_beds,already_sorted=True)
intergenic_beds = window_break(intergenic_beds,args.window_size)
#for i in intergenic_beds: print i.get_range_string()
sys.stderr.write("Get merged exons\n")
exon_beds = merge_ranges(exon_beds)
sys.stderr.write("Get introns\n")
intron_beds = subtract_ranges(gene_beds,exon_beds,already_sorted=True)
intron_beds = merge_ranges(intron_beds,already_sorted=True)
intron_beds = window_break(intron_beds,args.window_size)
sys.stderr.write("Going through short reads\n")
cmd = "sam_to_bed_depth.py "+args.bam_input
p = Popen(cmd.split(),stdout=PIPE)
for x in intron_beds: x.set_payload([]) # payloads are read depths
for x in intergenic_beds: x.set_payload([]) # payloads are read depths
for x in exon_beds: x.set_payload([]) # payloads are read depths
introndepth = []
intergenicdepth = []
exondepth = []
pseudoreadcount = 0
if not args.get_exons: exon_beds = []
section_count = 0
while True:
section_count += 1
line = p.stdout.readline()
if not line: break
f = line.split("\t")
depth = int(f[3])
curr = Bed(f[0],int(f[1]),int(f[2]))
if section_count %100==0: sys.stderr.write(curr.get_range_string()+" \r")
pseudoreadcount += depth
if len(exon_beds) > 0:
while curr.cmp(exon_beds[0]) > 0 and len(exon_beds) > 0: # we've passed the region
v = exon_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions: continue
av = average(v)
exondepth.append(av)
#print str(av)+" exonic "+v.get_range_string()
c = curr.cmp(exon_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(exon_beds[0])
for i in range(0,size): exon_beds[0].get_payload().append(depth)
if len(intron_beds) > 0:
while curr.cmp(intron_beds[0]) > 0 and len(intron_beds) > 0: # we've passed the region
v = intron_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions: continue
av = average(v)
introndepth.append(av)
#print str(av)+" intronic "+v.get_range_string()
c = curr.cmp(intron_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(intron_beds[0])
for i in range(0,size): intron_beds[0].get_payload().append(depth)
if len(intergenic_beds) > 0:
while curr.cmp(intergenic_beds[0]) > 0 and len(intergenic_beds) > 0: # we've passed the region
v = intergenic_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions: continue
av = average(v)
intergenicdepth.append(av)
display(curr,introndepth,intergenicdepth,pseudoreadcount,avglen)
#print str(av)+" intergenic "+v.get_range_string()
c = curr.cmp(intergenic_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(intergenic_beds[0])
for i in range(0,size): intergenic_beds[0].get_payload().append(depth)
#if c > 0: # we passed the intron
# v = intergenic_beds.pop(0)
# av = average(v)
# intergenicdepth.append(av)
# print str(av)+" intergenic "+v.get_range_string()
if args.use_off_regions:
for x in exon_beds: introndepth.append(average(x.get_payload()))
for x in intron_beds: introndepth.append(average(x.get_payload()))
for x in intergenic_beds: intergenicdepth.append(average(x.get_payload()))
p.communicate()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('gpd_input')
parser.add_argument('bam_input')
parser.add_argument('--intergenic_buffer', default=10000, type=int)
parser.add_argument('--window_size', default=10000, type=int)
parser.add_argument('--bin_size', default=1000, type=int)
parser.add_argument(
'--use_off_regions',
action='store_true',
help="Use a region even if there is no reads mapped to it.")
parser.add_argument('--get_exons', action='store_true')
args = parser.parse_args()
chr_beds = {}
gene_beds = []
exon_beds = []
sys.stderr.write("Reading genepred file\n")
asum = 0
atot = 0
with open(args.gpd_input) as inf:
for line in inf:
g = GenePredEntry(line)
asum += g.length()
atot += 1
grng = g.get_bed()
grng.direction = None
if grng.chr not in chr_beds:
chr_beds[grng.chr] = grng.copy()
chr_beds[grng.chr] = chr_beds[grng.chr].merge(grng)
gene_beds.append(grng)
for i in range(0, g.get_exon_count()):
erng = Bed(g.value('chrom'),
g.value('exonStarts')[i],
g.value('exonEnds')[i])
exon_beds.append(erng)
avglen = float(asum) / float(atot)
sys.stderr.write("Sorting gene bed\n")
gene_beds = sort_ranges(gene_beds)
gene_beds = merge_ranges(gene_beds, already_sorted=True)
sys.stderr.write("Sorting chromosome beds\n")
chr_beds = sort_ranges([chr_beds[x] for x in chr_beds.keys()])
sys.stderr.write("Sorting exon beds\n")
exon_beds = sort_ranges(exon_beds)
sys.stderr.write("Get padded genes\n")
padded_gene_beds = pad_ranges(gene_beds, args.intergenic_buffer, chr_beds)
padded_gene_beds = merge_ranges(padded_gene_beds, already_sorted=True)
sys.stderr.write("Get intergenic regions\n")
intergenic_beds = subtract_ranges(chr_beds,
padded_gene_beds,
already_sorted=True)
intergenic_beds = merge_ranges(intergenic_beds, already_sorted=True)
intergenic_beds = window_break(intergenic_beds, args.window_size)
#for i in intergenic_beds: print i.get_range_string()
sys.stderr.write("Get merged exons\n")
exon_beds = merge_ranges(exon_beds)
sys.stderr.write("Get introns\n")
intron_beds = subtract_ranges(gene_beds, exon_beds, already_sorted=True)
intron_beds = merge_ranges(intron_beds, already_sorted=True)
intron_beds = window_break(intron_beds, args.window_size)
sys.stderr.write("Going through short reads\n")
cmd = "sam_to_bed_depth.py " + args.bam_input
p = Popen(cmd.split(), stdout=PIPE)
for x in intron_beds:
x.set_payload([]) # payloads are read depths
for x in intergenic_beds:
x.set_payload([]) # payloads are read depths
for x in exon_beds:
x.set_payload([]) # payloads are read depths
introndepth = []
intergenicdepth = []
exondepth = []
pseudoreadcount = 0
if not args.get_exons: exon_beds = []
section_count = 0
while True:
section_count += 1
line = p.stdout.readline()
if not line: break
f = line.split("\t")
depth = int(f[3])
curr = Bed(f[0], int(f[1]), int(f[2]))
if section_count % 100 == 0:
sys.stderr.write(curr.get_range_string() + " \r")
pseudoreadcount += depth
if len(exon_beds) > 0:
while curr.cmp(exon_beds[0]) > 0 and len(
exon_beds) > 0: # we've passed the region
v = exon_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions:
continue
av = average(v)
exondepth.append(av)
#print str(av)+" exonic "+v.get_range_string()
c = curr.cmp(exon_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(exon_beds[0])
for i in range(0, size):
exon_beds[0].get_payload().append(depth)
if len(intron_beds) > 0:
while curr.cmp(intron_beds[0]) > 0 and len(
intron_beds) > 0: # we've passed the region
v = intron_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions:
continue
av = average(v)
introndepth.append(av)
#print str(av)+" intronic "+v.get_range_string()
c = curr.cmp(intron_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(intron_beds[0])
for i in range(0, size):
intron_beds[0].get_payload().append(depth)
if len(intergenic_beds) > 0:
while curr.cmp(intergenic_beds[0]) > 0 and len(
intergenic_beds) > 0: # we've passed the region
v = intergenic_beds.pop(0)
if len(v.get_payload()) == 0 and not args.use_off_regions:
continue
av = average(v)
intergenicdepth.append(av)
display(curr, introndepth, intergenicdepth, pseudoreadcount,
avglen)
#print str(av)+" intergenic "+v.get_range_string()
c = curr.cmp(intergenic_beds[0])
if c == 0: # overlaps with intron
size = curr.overlap_size(intergenic_beds[0])
for i in range(0, size):
intergenic_beds[0].get_payload().append(depth)
#if c > 0: # we passed the intron
# v = intergenic_beds.pop(0)
# av = average(v)
# intergenicdepth.append(av)
# print str(av)+" intergenic "+v.get_range_string()
if args.use_off_regions:
for x in exon_beds:
introndepth.append(average(x.get_payload()))
for x in intron_beds:
introndepth.append(average(x.get_payload()))
for x in intergenic_beds:
intergenicdepth.append(average(x.get_payload()))
p.communicate()
