def get_overlapping_genes(bamfh, read, gene_trees):
intervals = get_genomic_intervals(read)
# get read strand if it exists
strand = get_strand(read)
# get all genes compatible with intervals
hits = []
for interval in intervals:
hits.append(get_genes_at_interval(bamfh.getrname(read.rname),
start=interval[0],
end=interval[1],
strand=strand,
trees=gene_trees))
return hits
def get_overlapping_genes(bamfh, read, gene_trees):
intervals = get_genomic_intervals(read)
# get read strand if it exists
strand = get_strand(read)
# get all genes compatible with intervals
hits = []
for interval in intervals:
hits.append(get_genes_at_interval(bamfh.getrname(read.rname),
start=interval[0],
end=interval[1],
strand=strand,
trees=gene_trees))
return hits
def get_transcript_coords(bamfh, read, exon_intervals, exon_trees):
intervals = get_genomic_intervals(read)
# get read strand if it exists
strand = get_strand(read)
# get all transcripts compatible with first interval
txhits = []
for interval in intervals:
#print 'READ', read.is_read1, 'INTERVAL', interval
txhits.append(get_transcripts_at_interval(bamfh.getrname(read.rname),
start=interval[0],
end=interval[1],
strand=strand,
exon_intervals=exon_intervals,
exon_trees=exon_trees))
return txhits
