def test_load_CTNNB1_exon_from_transcript(): transcript_id = "ENST00000453024" exons = ensembl.get_exons_from_transcript(transcript_id) assert(exons.shape[0] == 17) transcript_id = "ENST00000405570" exons = ensembl.get_exons_from_transcript(transcript_id) assert(exons.shape[0] == 16)
def test_load_CTNNB1_exon_from_transcript_length(): transcript_id = 'ENST00000405570' transcript = ref_data.get_cdna(transcript_id) exons = ensembl.get_exons_from_transcript(transcript_id) exons['length'] = exons['seq_region_end_exon'] - exons['seq_region_start_exon'] + 1 assert(exons['length'].sum() == len(transcript)), exons
def test_get_3prime_utr_length_CTNNB1(): transcript_id = "ENST00000405570" exons = ensembl.get_exons_from_transcript(transcript_id) utr_length = ensembl.get_three_prime_utr_length(exons) print utr_length assert(utr_length == 11)
def test_get_3prime_utr_length_reverse_strand_CASP9(): transcript_id = "ENST00000333868" exons = ensembl.get_exons_from_transcript(transcript_id) utr_length = ensembl.get_three_prime_utr_length(exons, forward = False) print utr_length assert(utr_length == 673)
def test_get_3prime_utr_length_RET(): transcript_id = "ENST00000355710" exons = ensembl.get_exons_from_transcript(transcript_id) utr_length = ensembl.get_three_prime_utr_length(exons) print utr_length assert(utr_length == 2082)