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 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 do_buffer(buffer, txome, args):
results = []
for line_z in buffer:
z = line_z[1]
line = line_z[0]
gpd = GPD(line)
v = annotate_line(gpd, txome, args)
if not v: continue
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]
results.append(str(z)+"\t"+gpd.get_gene_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")
return results
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 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"
