def gtf_add_isoform(gtf, iso, out=sys.stdout, quiet=False):
isoforms = {}
if not quiet:
sys.stderr.write('Reading isoforms...\n')
for line in gzip_reader(iso):
if line[0] == '#':
continue
cols = line.rstrip().split('\t')
isoforms[cols[1]] = cols[0]
if not quiet:
sys.stderr.write('Reading/Writing GTF...\n')
for line in gzip_reader(gtf):
try:
comment = None
idx = line.find('#')
if idx > -1:
if idx == 0:
sys.stdout.write(line)
continue
comment = line[idx:]
line = line[:-idx]
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip(
).split('\t')
transcript_id = None
for key, val in [
x.split(' ')
for x in [x.strip() for x in attrs.split(';')] if x
]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == 'transcript_id':
transcript_id = val
if attrs[-1] != ';':
attrs = '%s;' % attrs
if transcript_id in isoforms:
attrs = '%s isoform_id "%s";' % (attrs,
isoforms[transcript_id])
out.write('\t'.join([
chrom, source, feature, start, end, score, strand, frame, attrs
]))
if comment:
out.write('\t%s' % comment)
out.write('\n')
except:
import traceback
sys.stderr.write('Error parsing line:\n%s\n' % line)
traceback.print_exc()
sys.exit(1)
def gtf_addreflink(gtf, reflink, out=sys.stdout, quiet=False, replace=False):
link_values = {}
if not quiet:
sys.stderr.write('Reading refLink...\n')
for line in gzip_reader(reflink):
cols = line.rstrip().split('\t')
link_values[cols[2]] = (cols[0], cols[6])
if not quiet:
sys.stderr.write('Reading GTF...\n')
for line in gzip_reader(gtf):
try:
comment = None
idx = line.find('#')
if idx > -1:
if idx == 0:
sys.stdout.write(line)
continue
comment = line[idx:]
line = line[:-idx]
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip().split('\t')
transcript_id = None
gene_id = None
for key, val in [x.split(' ') for x in [x.strip() for x in attrs.split(';')] if x]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == 'transcript_id':
transcript_id = val
elif key == 'gene_id':
gene_id = val
if attrs[-1] != ';':
attrs = '%s;' % attrs
if transcript_id in link_values:
if replace:
attrs = 'gene_id "%s"; transcript_id "%s"; gene_name "%s"; orig_gene_id "%s";' % (link_values[transcript_id][1], transcript_id, link_values[transcript_id][0], gene_id)
else:
extra = 'gene_name "%s"; isoform_id "%s";' % link_values[transcript_id]
attrs = '%s %s' % (attrs, extra)
out.write('\t'.join([chrom, source, feature, start, end, score, strand, frame, attrs]))
if comment:
out.write('\t%s' % comment)
out.write('\n')
except:
import traceback
sys.stderr.write('Error parsing line:\n%s\n' % line)
traceback.print_exc()
sys.exit(1)
def gtf_add_isoform(gtf, iso, out=sys.stdout, quiet=False):
isoforms = {}
if not quiet:
sys.stderr.write('Reading isoforms...\n')
for line in gzip_reader(iso):
if line[0] == '#':
continue
cols = line.rstrip().split('\t')
isoforms[cols[1]] = cols[0]
if not quiet:
sys.stderr.write('Reading/Writing GTF...\n')
for line in gzip_reader(gtf):
try:
comment = None
idx = line.find('#')
if idx > -1:
if idx == 0:
sys.stdout.write(line)
continue
comment = line[idx:]
line = line[:-idx]
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip().split('\t')
transcript_id = None
for key, val in [x.split(' ') for x in [x.strip() for x in attrs.split(';')] if x]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == 'transcript_id':
transcript_id = val
if attrs[-1] != ';':
attrs = '%s;' % attrs
if transcript_id in isoforms:
attrs = '%s isoform_id "%s";' % (attrs, isoforms[transcript_id])
out.write('\t'.join([chrom, source, feature, start, end, score, strand, frame, attrs]))
if comment:
out.write('\t%s' % comment)
out.write('\n')
except:
import traceback
sys.stderr.write('Error parsing line:\n%s\n' % line)
traceback.print_exc()
sys.exit(1)
def bedgraph_clean(bedgraph, chrom_sizes, out=sys.stdout):
refs = {}
with open(chrom_sizes) as f:
for line in f:
cols = line.strip().split("\t")
refs[cols[0]] = int(cols[1])
first = True
extra = ""
for line in gzip_reader(bedgraph, callback=lambda: extra):
if first:
out.write(line) # header
first = False
continue
cols = line.strip().split("\t")
ref = cols[0]
start = int(cols[1])
end = int(cols[2])
extra = "%s:%s-%s" % (ref, start, end)
if not ref in refs:
continue
if start >= refs[ref]:
# skip this... it makes no sense
continue
if end > refs[ref]:
# truncate this record...
cols[2] = refs[ref]
out.write("%s\n" % "\t".join([str(x) for x in cols]))
def gtf_add_xref(gtf, xref, column=4, out=sys.stdout, quiet=False):
gene_names = {}
if not quiet:
sys.stderr.write("Reading xref...\n")
for line in gzip_reader(xref):
if line[0] == "#":
continue
cols = line.rstrip().split("\t")
gene_names[cols[0]] = cols[column]
if not quiet:
sys.stderr.write("Reading/writing GTF...\n")
for line in gzip_reader(gtf):
try:
comment = None
idx = line.find("#")
if idx > -1:
if idx == 0:
sys.stdout.write(line)
continue
comment = line[idx:]
line = line[:-idx]
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip().split("\t")
transcript_id = None
for key, val in [x.split(" ") for x in [x.strip() for x in attrs.split(";")] if x]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == "transcript_id":
transcript_id = val
if attrs[-1] != ";":
attrs = "%s;" % attrs
if transcript_id in gene_names:
attrs = '%s gene_name "%s";' % (attrs, gene_names[transcript_id])
out.write("\t".join([chrom, source, feature, start, end, score, strand, frame, attrs]))
if comment:
out.write("\t%s" % comment)
out.write("\n")
except:
import traceback
sys.stderr.write("Error parsing line:\n%s\n" % line)
traceback.print_exc()
sys.exit(1)
def qseq_reader(fname=None, fileobj=None, quiet=False):
if not fileobj:
if not fname:
raise ValueError('Must pass fname or fileobj!')
for line in gzip_reader(fname, quiet=quiet):
yield QseqRecord(*line.strip().split('\t')[:11])
else:
for line in fileobj:
yield QseqRecord(*line.strip().split('\t')[:11])
def gtf_filter(fname, filters, out=sys.stdout):
for line in gzip_reader(fname):
cols = line.strip('\n').split('\t')
good = True
for filt in filters:
if not filt.process(cols):
good = False
break
if good:
out.write('%s\n' % '\t'.join([str(x) for x in cols]))
def gtf_filter(fname, filters, out=sys.stdout):
for line in gzip_reader(fname):
cols = line.strip('\n').split('\t')
good = True
for filt in filters:
cols = filt.process(cols)
if not cols:
good = False
break
if good:
out.write('%s\n' % '\t'.join([str(x) for x in cols]))
def gtf_remove_dup(fname, out=sys.stdout, quiet=False):
if not quiet:
sys.stderr.write('Reading GTF...\n')
dup_count = 0
good_count = 0
for line in gzip_reader(fname, quiet=quiet):
try:
if line[0] == '#':
out.write(line)
continue
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip().split('\t')
transcript_id = None
for key, val in [x.split(' ') for x in [x.strip() for x in attrs.split(';')] if x]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == 'transcript_id':
transcript_id = val
if '_dup' in transcript_id:
dup_count += 1
continue
good_count += 1
out.write(line)
except:
import traceback
sys.stderr.write('Error parsing line:\n%s\n' % line)
traceback.print_exc()
sys.exit(1)
if not quiet:
sys.stderr.write('Kept %s transcript/exon annotations\n' % good_count)
sys.stderr.write('Removed %s duplicate transcript/exon annotations\n' % dup_count)
return (good_count, dup_count)
def gtf_addreflink(gtf, reflink, out=sys.stdout, quiet=False, replace=False):
link_values = {}
if not quiet:
sys.stderr.write('Reading refLink...\n')
for line in gzip_reader(reflink):
cols = line.rstrip().split('\t')
link_values[cols[2]] = (cols[0], cols[6])
if not quiet:
sys.stderr.write('Reading GTF...\n')
for line in gzip_reader(gtf):
try:
comment = None
idx = line.find('#')
if idx > -1:
if idx == 0:
sys.stdout.write(line)
continue
comment = line[idx:]
line = line[:-idx]
chrom, source, feature, start, end, score, strand, frame, attrs = line.rstrip(
).split('\t')
transcript_id = None
gene_id = None
for key, val in [
x.split(' ')
for x in [x.strip() for x in attrs.split(';')] if x
]:
if val[0] == '"' and val[-1] == '"':
val = val[1:-1]
if key == 'transcript_id':
transcript_id = val
elif key == 'gene_id':
gene_id = val
if attrs[-1] != ';':
attrs = '%s;' % attrs
if transcript_id in link_values:
if replace:
attrs = 'gene_id "%s"; transcript_id "%s"; gene_name "%s"; orig_gene_id "%s";' % (
link_values[transcript_id][1], transcript_id,
link_values[transcript_id][0], gene_id)
else:
extra = 'gene_name "%s"; isoform_id "%s";' % link_values[
transcript_id]
attrs = '%s %s' % (attrs, extra)
out.write('\t'.join([
chrom, source, feature, start, end, score, strand, frame, attrs
]))
if comment:
out.write('\t%s' % comment)
out.write('\n')
except:
import traceback
sys.stderr.write('Error parsing line:\n%s\n' % line)
traceback.print_exc()
sys.exit(1)
