How to use the pyensembl.ensembl_grch38.transcripts_by_name function in pyensembl

def test_sequence_key_for_variant_on_transcript_deletion_reverse_strand():
    # delete start codon of TP53-001, which in reverse complement means
    # deleting the sequence "CAT"
    tp53_deletion = Variant(
        "17", 7676592, "CAT", "", ensembl_grch38)
    tp53_001 = ensembl_grch38.transcripts_by_name("TP53-001")[0]
    # Sequence of TP53 around start codon with 10 context nucleotides:
    # In [51]: t.sequence[190-10:190+13]
    # Out[51]: 'GGTCACTGCC_ATG_GAGGAGCCGC'
    eq_(tp53_001.sequence[190 - 10:190 + 13], "GGTCACTGCCATGGAGGAGCCGC")

    # get the 5 nucleotides before the variant and 10 nucleotides after
    sequence_key = ReferenceSequenceKey.from_variant_and_transcript(
        variant=tp53_deletion,
        transcript=tp53_001,
        context_size=10)

    expected_sequence_key = ReferenceSequenceKey(
        strand="-",
        sequence_before_variant_locus="GGTCACTGCC",
        sequence_at_variant_locus="ATG",
        sequence_after_variant_locus="GAGGAGCCGC")

def test_reference_coding_sequence_key_insertion_inside_start_codon():
    # insert nucleotide "C" in the middle of the start codon of TP53-001,
    # keeping only 1 nucleotide of context. In the reverse complement this
    # becomes 'T'>'TG'
    tp53_insertion = Variant(
        "17", 7676592, "T", "TG", ensembl_grch38)

    tp53_001 = ensembl_grch38.transcripts_by_name("TP53-001")[0]

    result = ReferenceCodingSequenceKey.from_variant_and_transcript(
        variant=tp53_insertion,
        transcript=tp53_001,
        context_size=1)
    assert result is None, "Expected result to be None when variant affects start codon"

def test_sequence_key_with_reading_frame_substitution_with_five_prime_utr():
    # Replace second codon of TP53-001 with 'CCC', the surrounding context
    # includes nucleotides from the 5' UTR. Since TP53 is on the negative
    # strand we have to take the reverse complement of the variant which turns
    # it into CTC>GGG
    tp53_substitution = Variant(
        "17", 7676589, "CTC", "GGG", ensembl_grch38)
    tp53_001 = ensembl_grch38.transcripts_by_name("TP53-001")[0]

    # Sequence of TP53 around second codon with 10 context nucleotides:
    # In [51]: t.sequence[193-10:193+13]
    # Out[51]: 'CACTGCCATGGAGGAGCCGCAGT'
    # Which can be split into the following parts:
    #  last 7 nt of 5' UTR: CACTGCC
    #  start codon: ATG (translates to M)
    #  2nd codon: GAG    <---- variant occurs here
    #  3rd codon: GAG
    #  4th codon: CCG
    #  5th codon:  CAG
    #  first nt of 6th codon: T
    result = ReferenceCodingSequenceKey.from_variant_and_transcript(
        variant=tp53_substitution,
        transcript=tp53_001,
        context_size=10)

def test_sequence_key_for_variant_on_transcript_insertion():
    # Insert 'CCC' after the 6th nucleotide of BRCA2-001's 5' UTR
    brca2_variant_insertion = Variant(
        "13", 32315479, "T", "TCCC", ensembl_grch38)
    brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0]
    # first 50 characters of BRCA2-001:
    #  "GGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTG"
    brca2_ref_seq = brca2_001.sequence[:50]
    eq_(brca2_ref_seq, "GGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTG")
    print(brca2_ref_seq)
    # get the 5 nucleotides before the variant and 10 nucleotides after
    sequence_key = ReferenceSequenceKey.from_variant_and_transcript(
        variant=brca2_variant_insertion,
        transcript=brca2_001,
        context_size=10)

    # expecting nothing at the variant locus since we're inserting between
    # two reference nucleotides
    expected_sequence_key = ReferenceSequenceKey(
        strand="+",
        sequence_before_variant_locus=brca2_ref_seq[:6],

def test_interbase_range_for_brca2_utr_deletion():
    # Deletion of the 6th nucleotide of BRCA2-001's 5' UTR
    brca2_deletion = Variant("13", 32315479, "T", "", ensembl_grch38)
    brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0]
    interbase_range = interbase_range_affected_by_variant_on_transcript(
        variant=brca2_deletion,
        transcript=brca2_001)
    print(interbase_range)
    eq_(interbase_range, (5, 6))

def test_interbase_range_for_brca2_utr_insertion():
    # T>TC insertion after the 6th nucleotide of BRCA2-001's 5' UTR
    brca2_insertion = Variant("13", 32315479, "T", "TC", ensembl_grch38)
    brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0]
    interbase_range = interbase_range_affected_by_variant_on_transcript(
        variant=brca2_insertion,
        transcript=brca2_001)
    print(interbase_range)
    eq_(interbase_range, (6, 6))

def test_interbase_range_for_brca2_utr_substitution():
    # rs769125639 is a simple T>A substitution in the 6th nucleotide of
    # BRCA2-001's 5' UTR
    brca2_variant_rs769125639 = Variant(
        "13", 32315479, "T", "A", ensembl_grch38)
    brca2_001 = ensembl_grch38.transcripts_by_name("BRCA2-001")[0]
    interbase_range = interbase_range_affected_by_variant_on_transcript(
        variant=brca2_variant_rs769125639,
        transcript=brca2_001)
    print(interbase_range)
    eq_(interbase_range, (5, 6))

def test_sequence_key_with_reading_frame_insertion_context_6nt_contains_start():
    # Insert nucleotide "T" after second codon of TP53-001,
    # but in this test we're going to only keep enough context to see
    # the start codon but none of the 5' UTR. In the reverse complement this
    # variant becomes CTC>CTCA
    tp53_insertion = Variant(
        "17", 7676586, "CTC", "CTCA", ensembl_grch38)

    tp53_001 = ensembl_grch38.transcripts_by_name("TP53-001")[0]
    # Sequence of TP53 around boundary of 2nd/3rd codons
    # with 6 context nucleotides:
    #   start codon: ATG (translates to M)
    #   2nd codon: GAG (translates to E)
    #   <---- insertion variant occurs between these two codons
    #   3rd codon: GAG
    #   4th codon: CCG

    result = ReferenceCodingSequenceKey.from_variant_and_transcript(
        variant=tp53_insertion,
        transcript=tp53_001,
        context_size=6)

    expected = ReferenceCodingSequenceKey(
        strand="-",
        sequence_before_variant_locus="ATGGAG",