def build_ivals(fp, genome_db, ests_db):
"""Generate aligned intervals based on the GMAP/GFF3 data in 'fp'.
Yields (pathname, ivals) where ivals is a list of interval pairs.
"""
for row in gff_parser.read(fp):
ivals = []
src_seq = get_src_sequence(genome_db, row)
dest_seq = get_dest_sequence(ests_db, row)
src_i = 0
dst_i = 0
for typ, m in gaps(row):
if typ == 'M': # full match
src_ival = src_seq[src_i:src_i + m]
dst_ival = dest_seq[dst_i:dst_i + m]
ivals.append((src_ival, dst_ival))
src_i += m
dst_i += m
elif typ == 'I': # insertion on dest seq
dst_i += m
elif typ == 'D': # insertion on src seq
src_i += m
else:
raise Exception, "unknown char in Gap attr: %s%d" % (typ, m)
yield row.attributes.ID, ivals
import sys
import gff_parser
import bincount
###
scores = bincount.BinCount()
paths_by_contig = {}
cdna_by_contig = {}
paths_by_cdna = {}
for row in gff_parser.read(open(sys.argv[1])):
scores.add(row.score)
contig = row.seqid
path = row.attributes.ID
cdna = row.attributes.Name
s = paths_by_contig.setdefault(contig, set())
s.add(path)
s = cdna_by_contig.setdefault(contig, set())
s.add(cdna)
s = paths_by_cdna.setdefault(cdna, set())
s.add(path)
###
scores.bin(1).write(open('scores.bin', 'w'), center=False)