예제 #1
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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)
예제 #2
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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
예제 #3
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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)
예제 #4
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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)
예제 #5
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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)