def get_info_string(self):
ostr = ""
ostr += "== FUZZY GENEPRED INFO ==" + "\n"
ostr += str(len(self.gpds)) + " total GPDs" + "\n"
totalbounds = Bed(self.start.chr, self.start.start - 1, self.end.end, self.start.direction)
ostr += totalbounds.get_range_string() + " total bounds\n"
ostr += "---- start ----" + "\n"
ostr += str(len(self.start.get_payload())) + " reads supporting start" + "\n"
ostr += " " + str(mean(self.start.get_payload())) + " mean" + "\n"
ostr += " " + str(mode(self.start.get_payload())) + " mode" + "\n"
ostr += " " + self.start.get_range_string() + " start range\n"
ostr += "---- end ----" + "\n"
ostr += str(len(self.end.get_payload())) + " reads supporting end" + "\n"
ostr += " " + str(mean(self.end.get_payload())) + " mean" + "\n"
ostr += " " + str(mode(self.end.get_payload())) + " mode" + "\n"
ostr += " " + self.end.get_range_string() + " end range\n"
ostr += "---- junctions ----" + "\n"
ostr += str(len(self.fuzzy_junctions)) + " total fuzzy junctions" + "\n"
cnt = 0
for j in self.fuzzy_junctions:
cnt += 1
ostr += (
" "
+ str(cnt)
+ ". "
+ str(mode(j.left.get_payload()["junc"]))
+ " ^ "
+ str(mode(j.right.get_payload()["junc"]))
+ "\n"
)
ostr += " " + j.left.get_range_string() + " ^ " + j.right.get_range_string() + "\n"
ostr += " " + str(len(j.left.get_payload()["junc"])) + " read support" + "\n"
if j.left.get_payload()["start"]:
ostr += " " + "---starts----" + "\n"
ostr += (
" "
+ str(len(j.left.get_payload()["start"].get_payload()))
+ " starts at "
+ j.left.get_payload()["start"].get_range_string()
+ "\n"
)
if j.right.get_payload()["end"]:
ostr += " " + "---ends----" + "\n"
ostr += (
" "
+ str(len(j.right.get_payload()["end"].get_payload()))
+ " ends at "
+ j.right.get_payload()["end"].get_range_string()
+ "\n"
)
return ostr
def get_info_string(self):
ostr = ''
ostr += "== FUZZY GENEPRED INFO ==" + "\n"
ostr += str(len(self.gpds)) + ' total GPDs' + "\n"
totalbounds = Bed(self.start.chr, self.start.start - 1, self.end.end,
self.start.direction)
ostr += totalbounds.get_range_string() + " total bounds\n"
ostr += '---- start ----' + "\n"
ostr += str(len(
self.start.get_payload())) + " reads supporting start" + "\n"
ostr += ' ' + str(mean(self.start.get_payload())) + ' mean' + "\n"
ostr += ' ' + str(mode(self.start.get_payload())) + ' mode' + "\n"
ostr += ' ' + self.start.get_range_string() + " start range\n"
ostr += '---- end ----' + "\n"
ostr += str(len(
self.end.get_payload())) + " reads supporting end" + "\n"
ostr += ' ' + str(mean(self.end.get_payload())) + ' mean' + "\n"
ostr += ' ' + str(mode(self.end.get_payload())) + ' mode' + "\n"
ostr += ' ' + self.end.get_range_string() + " end range\n"
ostr += '---- junctions ----' + "\n"
ostr += str(len(
self.fuzzy_junctions)) + ' total fuzzy junctions' + "\n"
cnt = 0
for j in self.fuzzy_junctions:
cnt += 1
ostr += ' ' + str(cnt) + '. ' + str(
mode(j.left.get_payload()['junc'])) + " ^ " + str(
mode(j.right.get_payload()['junc'])) + "\n"
ostr += " " + j.left.get_range_string(
) + " ^ " + j.right.get_range_string() + "\n"
ostr += " " + str(len(
j.left.get_payload()['junc'])) + " read support" + "\n"
if j.left.get_payload()['start']:
ostr += " " + "---starts----" + "\n"
ostr += " " + str(
len(j.left.get_payload()['start'].get_payload())
) + " starts at " + j.left.get_payload(
)['start'].get_range_string() + "\n"
if j.right.get_payload()['end']:
ostr += " " + "---ends----" + "\n"
ostr += " " + str(
len(j.right.get_payload()['end'].get_payload())
) + " ends at " + j.right.get_payload(
)['end'].get_range_string() + "\n"
return ostr
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()
