return (end - start + 1) / b.length
def overlap(db, feature):
overlaps = db.overlaps(feature)
if len(overlaps) >= args.min_overlap_count and \
len(overlaps) <= args.max_overlap_count:
valid = []
for o in overlaps:
amt = calc_overlap(o, feature)
if amt >= args.min_overlap and amt <= args.max_overlap:
valid.append(o.ID)
if len(valid) > 0:
feature.attributes['overlaps'] = ','.join(valid)
if __name__ == '__main__':
args = parser.parse_args()
db = PositionDatabase(Feature.from_file(args.reference))
chromosomes, genes, transcripts = build_tree(Feature.from_file(args.gff))
for t in transcripts.values():
overlap(db, t)
flat = flatten_tree(chromosomes)
print '\n'.join([str(f) for f in flat])
return (end - start + 1) / b.length
def overlap(db, feature):
overlaps = db.overlaps(feature)
if len(overlaps) >= args.min_overlap_count and \
len(overlaps) <= args.max_overlap_count:
valid = []
for o in overlaps:
amt = calc_overlap(o, feature)
if amt >= args.min_overlap and amt <= args.max_overlap:
valid.append(o.ID)
if len(valid) > 0:
feature.attributes['overlaps'] = ','.join(valid)
if __name__ == '__main__':
args = parser.parse_args()
db = PositionDatabase(Feature.from_file(args.reference))
chromosomes, genes, transcripts = build_tree(Feature.from_file(args.gff))
for t in transcripts.values():
overlap(db, t)
flat = flatten_tree(chromosomes)
print '\n'.join([str(f) for f in flat])
ID = x.findtext('.//Iteration_query-def')
query_len = x.findtext('.//Iteration_query-len')
hits = x.findall('.//Hit')
for hit in hits:
hit_def = hit.findtext('.//Hit_def')
hit_len = hit.findtext('.//Hit_len')
identity = hit.findtext('.//Hsp_identity')
align_len = hit.findtext('.//Hsp_align-len')
if identity != align_len:
midline = hit.findtext('.//Hsp_midline')
gap_match = rx.search(midline)
if gap_match:
continue
p = (float(identity) / float(hit_len)) * (float(identity) / float(query_len))
if p >= args.min_match:
try:
t = transcripts[ID]
except KeyError:
pass
else:
try:
t.attributes['blasts_to'] = ','.join([t.attributes['blasts_to'],
hit_def])
except KeyError:
t.attributes['blasts_to'] = hit_def
for f in flatten_tree(chromosomes):
print f