def to_gtf_features(self, source=None, score=1000):
if source is None:
source = 'assemblyline'
# transcript feature
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'transcript'
f.start = self.start
f.end = self.end
f.score = score
f.strand = strand_int_to_str(self.strand)
f.phase = '.'
f.attrs = self.attrs
features = [f]
# exon features
for i, e in enumerate(self.exons):
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'exon'
f.start = e.start
f.end = e.end
f.score = score
f.strand = strand_int_to_str(self.strand)
f.phase = '.'
f.attrs = self.attrs.copy()
f.attrs["exon_number"] = i
features.append(f)
return features
def to_gtf_features(self, source=None, score=1000):
if source is None:
source = 'assemblyline'
# transcript feature
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'transcript'
f.start = self.start
f.end = self.end
f.score = score
f.strand = strand_int_to_str(self.strand)
f.phase = '.'
f.attrs = self.attrs
features = [f]
# exon features
for i,e in enumerate(self.exons):
f = GTFFeature()
f.seqid = self.chrom
f.source = source
f.feature_type = 'exon'
f.start = e.start
f.end = e.end
f.score = score
f.strand = strand_int_to_str(self.strand)
f.phase = '.'
f.attrs = self.attrs.copy()
f.attrs["exon_number"] = i
features.append(f)
return features
