Python AnnotationRequestFactory Examples

Example #1

def test_subs_3_prime_side(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:80", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect is None

    variant = Variant(loc="1:79", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

    variant = Variant(loc="1:78", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

    variant = Variant(loc="1:77", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

Example #2

def test_deletion_5_prime_side(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:70", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect is None

    variant = Variant(loc="1:71", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

    variant = Variant(loc="1:72", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

    variant = Variant(loc="1:73", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "intron"

Example #3

File: test_coding_tests.py Project: iossifovlab/gpf

def test_deletion_3_prime_side(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:80", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding"

    variant = Variant(loc="1:79", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

    variant = Variant(loc="1:78", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

    variant = Variant(loc="1:77", ref="0", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

Example #4

File: test_coding_tests.py Project: iossifovlab/gpf

def test_subs_5_prime_side(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:70", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding"

    variant = Variant(loc="1:71", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

    variant = Variant(loc="1:72", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

    variant = Variant(loc="1:73", ref="A", alt="G")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model
    )
    effect = effect_checker.get_effect(request)
    assert effect.effect == "non-coding-intron"

Example #5

File: test_annotation_request.py Project: iossifovlab/gpf

def test_exonic_distance(annotator, transcript_model):
    variant = Variant(loc="1:64", ref="A", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    assert request.get_exonic_distance(60, 61) == 1
    assert request.get_exonic_distance(60, 70) == 10
    assert request.get_exonic_distance(60, 80) == 11
    assert request.get_exonic_distance(70, 80) == 1

Example #6

File: test_start_loss_tests.py Project: iossifovlab/gpf

def test_negative_deletion_at_start(annotator, negative_transcript_model,
                                    effect_checker):
    variant = Variant(loc="1:109", ref="ABC", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, negative_transcript_model)
    effect = effect_checker.get_effect(request)

    assert effect.effect == "noStart"

Example #7

File: test_start_loss_tests.py Project: iossifovlab/gpf

def test_possitive_insertion_after_start(annotator, possitive_transcript_model,
                                         effect_checker):
    variant = Variant(loc="1:68", ref="", alt="ABC")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, possitive_transcript_model)
    effect = effect_checker.get_effect(request)

    assert effect is None

Example #8

File: test_protein_change_tests.py Project: iossifovlab/gpf

def test_multiple_codons_nonsense(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:65", ref="ABCDEF", alt="EndPBC")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    request.cod2aa = lambda codon: codon
    effect = effect_checker.get_effect(request)

    assert effect.effect == "nonsense"

Example #9

File: test_protein_change_tests.py Project: iossifovlab/gpf

def test_synonymous(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:65", ref="ABC", alt="End")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    request.cod2aa = lambda codon: "Asn"
    effect = effect_checker.get_effect(request)

    assert effect.effect == "synonymous"

Example #10

File: test_stop_loss_tests.py Project: iossifovlab/gpf

def test_negative_deletion_before_end(annotator, negative_transcript_model,
                                      effect_checker):
    variant = Variant(loc="1:62", ref="ABC", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, negative_transcript_model)
    effect = effect_checker.get_effect(request)

    assert effect is None

Example #11

File: test_utr_tests.py Project: iossifovlab/gpf

def test_deletion_before_start(annotator, transcript_model, effect_checker):
    variant = Variant(loc="1:65", ref="A", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    effect = effect_checker.get_effect(request)

    assert effect.effect == "5'UTR"
    assert effect.dist_from_coding == 11

Example #12

File: test_utr_tests.py Project: iossifovlab/gpf

def test_deletion_after_end_last_exon(annotator, transcript_model,
                                      effect_checker):
    variant = Variant(loc="1:151", ref="A", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    effect = effect_checker.get_effect(request)

    assert effect.effect == "3'UTR"
    assert effect.dist_from_coding == 7

Example #13

File: test_annotation_request.py Project: iossifovlab/gpf

def test_exonic_pos_last_exon(annotator, transcript_model):
    variant = Variant(loc="1:110", ref="A", alt="")
    request = AnnotationRequestFactory.create_annotation_request(
        annotator, variant, transcript_model)
    assert request.get_exonic_position() == 33
    assert request.get_exonic_length() == 33