def get_merged_exons(self):
"""Returns a list of non-redundant exon coordinates for this
gene. Overlapping exons are merged."""
# get redundant, sorted list of all exons
exon_list = []
for tr in self.transcripts:
exon_list.extend(tr.exons)
coord.sort_coords(exon_list, use_strand=False)
# create coordinate group from first exon
cur_exon = coord.CoordGroup(exon_list[0])
merged_exons = [cur_exon]
# merge overlapping exons
for ex in exon_list[1:]:
if ex.overlaps(cur_exon):
# expand current exon
cur_exon.add_coord(ex)
else:
# new exon group
cur_exon = coord.CoordGroup(ex)
merged_exons.append(cur_exon)
return merged_exons
def group_transcripts(trs):
"""Creates a list of genes created from overlapping sets of
transcripts. The provided list of transcripts is sorted in-place
by this function."""
if len(trs) == 0:
return []
# sort transcripts, and then find overlapping transcripts on same strand
coord.sort_coords(trs, use_strand=True)
# start first gene with first transcript
cur_gene = Gene([trs[0]])
genes = [cur_gene]
for tr in trs[1:]:
if tr.overlaps(cur_gene, use_strand=True):
# keep adding overlapping transcripts to current gene
cur_gene.add_transcript(tr)
else:
# start a new gene
cur_gene = Gene([tr])
genes.append(cur_gene)
return genes
