def annotate_line(inputs):
global txome
(line,z,args) = inputs
gpd = GPD(line)
gpd.set_payload(z)
v = gpd.get_range()
if v.chr not in txome: return None
possible = [x.get_payload() for x in txome[v.chr] if x.overlaps(v)]
candidates = []
if len(possible) == 0: return None
for tx in possible:
eo = None
full = False
subset = False
econsec = 1
if tx.get_exon_count() == 1 or gpd.get_exon_count() == 1:
eo = gpd.exon_overlap(tx,single_minover=100,single_frac=0.5)
else:
eo = gpd.exon_overlap(tx,multi_minover=10,multi_endfrac=0,multi_midfrac=0.8,multi_consec=False)
if eo.is_full_overlap():
full = True
if eo.is_subset():
subset = True
if eo:
econsec = eo.consecutive_exon_count()
if not eo: continue
ecnt = eo.match_exon_count()
osize = gpd.overlap_size(tx)
candidates.append([full,subset,ecnt,econsec,gpd.get_exon_count(),tx.get_exon_count(),osize,gpd.get_length(),tx.get_length(),tx])
if len(candidates)==0: return None
bests = sorted(candidates,key=lambda x: (-x[0],-x[1],-x[3],-x[2],-min(float(x[6])/float(x[7]),float(x[6])/float(x[8]))))
#line_z
v = bests[0]
### we have the annotation
z = gpd.get_payload()
#line = line_z[0]
#gpd = GPD(line)
if not v: return None
type = 'partial'
if v[0]: type = 'full'
exon_count = v[2]
most_consecutive_exons = v[3]
read_exon_count = v[4]
tx_exon_count = v[5]
overlap_size = v[6]
read_length = v[7]
tx_length = v[8]
return str(z)+"\t"+gpd.get_transcript_name()+"\t"+v[9].get_gene_name()+"\t"+v[9].get_transcript_name()+"\t"+type+"\t"+\
str(exon_count)+"\t"+str(most_consecutive_exons)+"\t"+str(read_exon_count)+"\t"+str(tx_exon_count)+"\t"+\
str(overlap_size)+"\t"+str(read_length)+"\t"+str(tx_length)+"\t"+gpd.get_range().get_range_string()+"\t"+v[9].get_range().get_range_string()+"\t"+str(v[9].get_payload())+"\n"
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):
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 annotate_line(inputs):
global txome
(line, z, args) = inputs
gpd = GPD(line)
gpd.set_payload(z)
v = gpd.get_range()
if v.chr not in txome: return None
possible = [x.get_payload() for x in txome[v.chr] if x.overlaps(v)]
candidates = []
if len(possible) == 0: return None
for tx in possible:
eo = None
full = False
subset = False
econsec = 1
if tx.get_exon_count() == 1 or gpd.get_exon_count() == 1:
eo = gpd.exon_overlap(tx, single_minover=100, single_frac=0.5)
else:
eo = gpd.exon_overlap(tx,
multi_minover=10,
multi_endfrac=0,
multi_midfrac=0.8,
multi_consec=False)
if eo.is_full_overlap():
full = True
if eo.is_subset():
subset = True
if eo:
econsec = eo.consecutive_exon_count()
if not eo: continue
ecnt = eo.match_exon_count()
osize = gpd.overlap_size(tx)
candidates.append([
full, subset, ecnt, econsec,
gpd.get_exon_count(),
tx.get_exon_count(), osize,
gpd.get_length(),
tx.get_length(), tx
])
if len(candidates) == 0: return None
bests = sorted(candidates,
key=lambda x: (-x[0], -x[1], -x[3], -x[2], -min(
float(x[6]) / float(x[7]),
float(x[6]) / float(x[8]))))
#line_z
v = bests[0]
### we have the annotation
z = gpd.get_payload()
#line = line_z[0]
#gpd = GPD(line)
if not v: return None
type = 'partial'
if v[0]: type = 'full'
exon_count = v[2]
most_consecutive_exons = v[3]
read_exon_count = v[4]
tx_exon_count = v[5]
overlap_size = v[6]
read_length = v[7]
tx_length = v[8]
return str(z)+"\t"+gpd.get_transcript_name()+"\t"+v[9].get_gene_name()+"\t"+v[9].get_transcript_name()+"\t"+type+"\t"+\
str(exon_count)+"\t"+str(most_consecutive_exons)+"\t"+str(read_exon_count)+"\t"+str(tx_exon_count)+"\t"+\
str(overlap_size)+"\t"+str(read_length)+"\t"+str(tx_length)+"\t"+gpd.get_range().get_range_string()+"\t"+v[9].get_range().get_range_string()+"\t"+str(v[9].get_payload())+"\n"
