def main(args):
of = sys.stdout
if args.output:
if re.search('\.gz$', args.output):
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
#read the reference gpd
rinf = None
global txome
txome = {}
if re.search('\.gz$', args.reference):
rinf = gzip.open(args.reference)
else:
rinf = open(args.reference)
sys.stderr.write("Reading in reference\n")
z = 0
# populate txome with reference transcripts for each chromosome
for line in rinf:
z += 1
gpd = GPD(line)
gpd.set_payload(z)
if z % 100 == 0: sys.stderr.write(str(z) + " \r")
if gpd.value('chrom') not in txome: txome[gpd.value('chrom')] = []
r = gpd.get_range()
r.set_payload(gpd)
txome[gpd.value('chrom')].append(r)
rinf.close()
sys.stderr.write(str(z) + " \r")
sys.stderr.write("\n")
inf = sys.stdin
if args.input != '-':
if re.search('\.gz$', args.input):
inf = gzip.open(args.input)
else:
inf = open(args.input)
#def annotate_line(gpd,txome,args):
sys.stderr.write("annotating\n")
p = Pool(processes=args.threads)
csize = 100
#for v in generate_tx(inf,args):
# res = annotate_line(v)
# if not res: continue
# print res.rstrip()
results2 = p.imap(func=annotate_line,
iterable=generate_tx(inf, args),
chunksize=csize)
#sys.stderr.write("done map\n")
for res in results2:
if not res: continue
of.write(res)
of.close()
def main(args):
of = sys.stdout
if args.output:
if re.search('\.gz$',args.output):
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
#read the reference gpd
rinf = None
global txome
txome = {}
if re.search('\.gz$',args.reference):
rinf = gzip.open(args.reference)
else:
rinf = open(args.reference)
sys.stderr.write("Reading in reference\n")
z = 0
# populate txome with reference transcripts for each chromosome
for line in rinf:
z += 1
gpd = GPD(line)
gpd.set_payload(z)
if z%100 == 0: sys.stderr.write(str(z)+" \r")
if gpd.value('chrom') not in txome: txome[gpd.value('chrom')] = []
r = gpd.get_range()
r.set_payload(gpd)
txome[gpd.value('chrom')].append(r)
rinf.close()
sys.stderr.write(str(z)+" \r")
sys.stderr.write("\n")
inf = sys.stdin
if args.input != '-':
if re.search('\.gz$',args.input):
inf = gzip.open(args.input)
else:
inf = open(args.input)
#def annotate_line(gpd,txome,args):
sys.stderr.write("annotating\n")
p = Pool(processes=args.threads)
csize = 100
#for v in generate_tx(inf,args):
# res = annotate_line(v)
# if not res: continue
# print res.rstrip()
results2 = p.imap(func=annotate_line,iterable=generate_tx(inf,args),chunksize=csize)
#sys.stderr.write("done map\n")
for res in results2:
if not res: continue
of.write(res)
of.close()
def main(args):
of = sys.stdout
if args.output:
if args.output[-3:] == '.gz':
of = gzip.open(args.output, 'w')
color = '0,0,0'
if args.color:
if args.color == 'blue':
color = '67,162,202'
elif args.color == 'green':
color = '49,163,84'
elif args.color == 'orange':
color = '254,178,76'
elif args.color == 'purple':
color = '136,86,167'
elif args.color == 'red':
color = '240,59,32'
# set up the header if one is desired
header = ''
if not args.noheader:
newname = 'longreads'
m = re.search('([^\/]+)$', args.input)
if m:
newname = m.group(1)
newname = re.sub('[\s]+', '_', newname)
if args.headername:
newname = args.headername
elif args.input == '-':
newname = 'STDIN'
header += "track\tname=" + newname + "\t"
description = newname + ' GenePred Entries'
if args.headerdescription:
description = args.headerdescription
header += 'description="' + description + '"' + "\t"
header += 'itemRgb="On"'
of.write(header + "\n")
gpd_handle = sys.stdin
if args.input != '-':
if args.input[-3:] == '.gz':
gpd_handle = gzip.open(args.input)
else:
gpd_handle = open(args.input)
gs = GPDStream(gpd_handle)
#with gpd_handle as infile:
for gpd in gs:
#for line in infile:
#if re.match('^#',line):
# continue
#genepred_entry = GenePredBasics.line_to_entry(line)
if args.minintron:
gpd = GPD(gpd.smooth_gaps(args.minintron).get_gpd_line())
exoncount = gpd.get_exon_count()
ostring = gpd.value('chrom') + "\t"
ostring += str(gpd.value('exonStarts')[0]) + "\t"
ostring += str(gpd.value('exonEnds')[exoncount - 1]) + "\t"
if args.namefield == 1:
ostring += gpd.value('gene_name') + "\t"
else:
ostring += gpd.value('name')
ostring += '1000' + "\t"
ostring += gpd.value('strand') + "\t"
ostring += str(gpd.value('exonStarts')[0]) + "\t"
ostring += str(gpd.value('exonEnds')[exoncount - 1]) + "\t"
ostring += color + "\t"
ostring += str(exoncount) + "\t"
for i in range(0, exoncount):
ostring += str(
gpd.value('exonEnds')[i] - gpd.value('exonStarts')[i]) + ','
ostring += "\t"
for i in range(0, exoncount):
ostring += str(
gpd.value('exonStarts')[i] - gpd.value('exonStarts')[0]) + ','
of.write(ostring + "\n")
#for i in range(0,len(genepred_entry['exonStarts'])):
gpd_handle.close()
of.close()
def main(args):
global of
if args.output:
if re.search('\.gz$', args.output):
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
#read the reference gpd
rinf = None
txome = {}
if re.search('\.gz$', args.reference):
rinf = gzip.open(args.reference)
else:
rinf = open(args.reference)
sys.stderr.write("Reading in reference\n")
z = 0
for line in rinf:
z += 1
gpd = GPD(line)
gpd.set_payload(z)
if z % 100 == 0: sys.stderr.write(str(z) + " \r")
if gpd.value('chrom') not in txome: txome[gpd.value('chrom')] = []
r = gpd.get_range()
r.set_payload(gpd)
txome[gpd.value('chrom')].append(r)
rinf.close()
sys.stderr.write(str(z) + " \r")
sys.stderr.write("\n")
inf = sys.stdin
if args.input != '-':
if re.search('\.gz$', args.input):
inf = gzip.open(args.input)
else:
inf = open(args.input)
z = 0
chroms = {}
sys.stderr.write("Buffering reads\n")
for line in inf:
z += 1
m = re.match('[^\t]*\t[^\t]*\t([^\t]+)', line)
chrom = m.group(1)
if z % 100 == 0: sys.stderr.write(str(z) + " \r")
if chrom not in chroms:
chroms[chrom] = []
chroms[chrom].append([line, z])
sys.stderr.write("\n")
sys.stderr.write("Finished buffering reads\n")
if args.threads > 1:
p = Pool(processes=args.threads)
results = []
global chrtotal
chrtotal = len(chroms)
for chrom in chroms:
if chrom not in txome: continue
if args.threads > 1:
v = p.apply_async(do_buffer,
args=(chroms[chrom], {
chrom: txome[chrom]
}, args),
callback=do_out)
results.append(v)
else:
v = do_buffer(chroms[chrom], {chrom: txome[chrom]}, args)
results.append(Queue(v))
do_out(v)
if args.threads > 1:
p.close()
p.join()
sys.stderr.write("\n")
for res in [x.get() for x in results]:
for oline in res:
of.write(oline)
inf.close()
of.close()
def main(args):
of = sys.stdout
if args.output:
if args.output[-3:]=='.gz':
of = gzip.open(args.output,'w')
color = '0,0,0'
if args.color:
if args.color == 'blue':
color = '67,162,202'
elif args.color == 'green':
color = '49,163,84'
elif args.color == 'orange':
color = '254,178,76'
elif args.color == 'purple':
color = '136,86,167'
elif args.color == 'red':
color = '240,59,32'
# set up the header if one is desired
header = ''
if not args.noheader:
newname = 'longreads'
m = re.search('([^\/]+)$',args.input)
if m:
newname = m.group(1)
newname = re.sub('[\s]+','_',newname)
if args.headername:
newname = args.headername
elif args.input == '-':
newname = 'STDIN'
header += "track\tname="+newname+"\t"
description = newname+' GenePred Entries'
if args.headerdescription:
description = args.headerdescription
header += 'description="'+description + '"'+"\t"
header += 'itemRgb="On"'
of.write(header+"\n")
gpd_handle = sys.stdin
if args.input != '-':
if args.input[-3:]=='.gz':
gpd_handle = gzip.open(args.input)
else:
gpd_handle = open(args.input)
gs = GPDStream(gpd_handle)
#with gpd_handle as infile:
for gpd in gs:
#for line in infile:
#if re.match('^#',line):
# continue
#genepred_entry = GenePredBasics.line_to_entry(line)
if args.minintron:
gpd = GPD(gpd.smooth_gaps(args.minintron).get_gpd_line())
exoncount = gpd.get_exon_count()
ostring = gpd.value('chrom') + "\t"
ostring += str(gpd.value('exonStarts')[0]) + "\t"
ostring += str(gpd.value('exonEnds')[exoncount-1]) + "\t"
if args.namefield == 1:
ostring += gpd.value('gene_name') + "\t"
else:
ostring += gpd.value('name')
ostring += '1000' + "\t"
ostring += gpd.value('strand') + "\t"
ostring += str(gpd.value('exonStarts')[0]) + "\t"
ostring += str(gpd.value('exonEnds')[exoncount-1]) + "\t"
ostring += color+"\t"
ostring += str(exoncount) + "\t"
for i in range(0,exoncount):
ostring += str(gpd.value('exonEnds')[i]-gpd.value('exonStarts')[i]) + ','
ostring += "\t"
for i in range(0,exoncount):
ostring += str(gpd.value('exonStarts')[i]-gpd.value('exonStarts')[0])+','
of.write(ostring+"\n")
#for i in range(0,len(genepred_entry['exonStarts'])):
gpd_handle.close()
of.close()
