def fromGTF(cls, gtf_rows):
ob = cls()
ob.transcripts = sorted([Transcript.fromGTF(rows) for rows in iter.groupBy(gtf_rows, "transcript_id")])
ob.range = range.bounds([transcript.range for transcript in ob.transcripts])
ob.chromosome = ob.transcripts[0].chromosome
ob.strand = ob.transcripts[0].strand
ob.name = ob.transcripts[0].gene
return ob
def fromGTF(cls, gtf_rows):
ob = cls()
ob.cds = [row.range for row in itertools.ifilter(lambda row: row.feature == "CDS", gtf_rows)]
ob.exons = [row.range for row in itertools.ifilter(lambda row: row.feature == "exon", gtf_rows)]
ob.name = gtf_rows[0].transcript_id
ob.gene = gtf_rows[0].gene_id
ob.strand = gtf_rows[0].strand
ob.chromosome = gtf_rows[0].seq_id
ob.range = range.bounds(ob.exons)
return ob