def main(parser):
args = parser.parse_args()
lines = utils.tab_line_gen(args.infile)
clustered = utils.cluster_gtf(lines)
reptypes = utils.by_attribute(clustered, 'repType')
catcount = Counter()
newlines = []
for cnum, c in clustered.iteritems():
c.sort(key=lambda x: int(x[3]))
cluster_id = '%s_%04d' % (args.prefix, int(cnum))
# Categorize cluster according to repeat types and orientation
if reptypes[cnum] == ['ltr', 'internal', 'ltr']:
category = 'prototype'
elif reptypes[cnum] == ['ltr', 'internal'
] or reptypes[cnum] == ['internal', 'ltr']:
category = 'oneside'
elif reptypes[cnum] == ['internal']:
category = 'soloint'
elif reptypes[cnum] == ['ltr']:
category = 'sololtr'
else:
category = 'unusual'
catcount[category] += 1
# Create the parent (merged) annotation
pstart = min(int(l[3]) for l in c)
pend = max(int(l[4]) for l in c)
strands = set(l[6] for l in c)
if len(strands) == 1: pstrand = strands.pop()
else: pstrand = '.' # Strand is ambiguous
pcov = utils.covered_len(c)
pattr = 'name "%s"; category "%s"; nfeats "%d"; length "%d"; cov "%d";' % (
cluster_id, category, len(c), (pend - pstart), pcov)
pline = [
c[0][0], 'merged', 'gene',
str(pstart),
str(pend), '.', pstrand, '.', pattr
]
newlines.append(pline)
for l in c:
l[1] = category
attr = dict(re.findall('(\S+)\s+"([\s\S]+?)";', l[8]))
if 'gene_id' in attr: del attr['gene_id']
if 'transcript_id' in attr: del attr['transcript_id']
l[8] = 'gene_id "%s"; transcript_id "%s"; ' % (cluster_id,
cluster_id)
l[8] = l[8] + ' '.join('%s "%s";' % (k, v)
for k, v in attr.iteritems())
newlines.append(l[:-1])
for l in utils.sort_gtf(newlines):
print >> args.outfile, '\t'.join(l)
for cat in ['prototype', 'oneside', 'soloint', 'sololtr', 'unusual']:
print >> sys.stderr, '%s: %d' % (cat, catcount[cat])
def make_mergeline(clust, name, category):
nm_spos = min(int(l[3]) for l in clust)
nm_epos = max(int(l[4]) for l in clust)
nm_strand = set(l[6] for l in clust)
nm_strand = nm_strand.pop() if len(nm_strand) == 1 else '.'
nm_cov = utils.covered_len(clust)
nm_attr = 'name "%s"; category "%s"; nfeats "%d"; length "%d"; cov "%d";' % (name, category, len(clust), (nm_epos-nm_spos), nm_cov)
nm = [clust[0][0], 'merged', 'gene', str(nm_spos), str(nm_epos), '.', nm_strand, '.', nm_attr]
return nm
def make_mergeline(clust, name, category):
nm_spos = min(int(l[3]) for l in clust)
nm_epos = max(int(l[4]) for l in clust)
nm_strand = set(l[6] for l in clust)
nm_strand = nm_strand.pop() if len(nm_strand) == 1 else '.'
nm_cov = utils.covered_len(clust)
nm_attr = 'name "%s"; category "%s"; nfeats "%d"; length "%d"; cov "%d";' % (
name, category, len(clust), (nm_epos - nm_spos), nm_cov)
nm = [
clust[0][0], 'merged', 'gene',
str(nm_spos),
str(nm_epos), '.', nm_strand, '.', nm_attr
]
return nm
def main(parser):
args = parser.parse_args()
lines = utils.tab_line_gen(args.infile)
clustered = utils.cluster_gtf(lines)
reptypes = utils.by_attribute(clustered, 'repType')
catcount = Counter()
newlines = []
for cnum,c in clustered.iteritems():
c.sort(key=lambda x:int(x[3]))
cluster_id = '%s_%04d' % (args.prefix,int(cnum))
# Categorize cluster according to repeat types and orientation
if reptypes[cnum] == ['ltr','internal','ltr']:
category = 'prototype'
elif reptypes[cnum] == ['ltr','internal'] or reptypes[cnum] == ['internal','ltr']:
category = 'oneside'
elif reptypes[cnum] == ['internal']:
category = 'soloint'
elif reptypes[cnum] == ['ltr']:
category = 'sololtr'
else:
category = 'unusual'
catcount[category] += 1
# Create the parent (merged) annotation
pstart = min(int(l[3]) for l in c)
pend = max(int(l[4]) for l in c)
strands = set(l[6] for l in c)
if len(strands)==1: pstrand = strands.pop()
else: pstrand = '.' # Strand is ambiguous
pcov = utils.covered_len(c)
pattr = 'name "%s"; category "%s"; nfeats "%d"; length "%d"; cov "%d";' % (cluster_id, category, len(c), (pend-pstart), pcov)
pline = [c[0][0], 'merged', 'gene', str(pstart), str(pend), '.', pstrand, '.', pattr]
newlines.append(pline)
for l in c:
l[1] = category
attr = dict(re.findall('(\S+)\s+"([\s\S]+?)";',l[8]))
if 'gene_id' in attr: del attr['gene_id']
if 'transcript_id' in attr: del attr['transcript_id']
l[8] = 'gene_id "%s"; transcript_id "%s"; ' % (cluster_id,cluster_id)
l[8] = l[8] + ' '.join('%s "%s";' % (k,v) for k,v in attr.iteritems())
newlines.append(l[:-1])
for l in utils.sort_gtf(newlines):
print >>args.outfile, '\t'.join(l)
for cat in ['prototype','oneside','soloint','sololtr','unusual']:
print >>sys.stderr, '%s: %d' % (cat, catcount[cat])
