Python GoRule30の例

コード例 #1

ファイル: test_qc.py プロジェクト: deepakunni3/ontobio

def test_gorule30():
    assoc = make_annotation(references="GO_REF:0000033").associations[0]

    config = assocparser.AssocParserConfig(goref_metadata={
        "goref-0000033": {
            "authors":
            "Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
            "id": "GO_REF:0000033",
            "is_obsolete": True
        }
    },
                                           rule_set=assocparser.RuleSet.ALL)

    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = [
        Curie.from_str("GO_PAINT:0000000")
    ]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = [
        Curie.from_str("FOO:123"),
        Curie.from_str("GO_REF:0000033")
    ]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = [Curie.from_str("FOO:123")]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.PASS

コード例 #2

ファイル: test_qc.py プロジェクト: robertdigital/ontobio

def test_gorule30():
    a = ["blah"] * 15
    a[3] = ""
    a[5] = "GO_REF:0000033"
    a[8] = "P"
    assoc = gafparser.to_association(a).associations[0]

    config = assocparser.AssocParserConfig(
        goref_metadata={
            "goref-0000033": {
                "authors":
                "Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
                "id": "GO_REF:0000033",
                "is_obsolete": True
            }
        })

    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = ["GO_PAINT:0000000"]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = ["FOO:123", "GO_REF:0000033"]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.WARNING

    assoc.evidence.has_supporting_reference = ["FOO:123"]
    test_result = qc.GoRule30().test(assoc, config)
    assert test_result.result_type == qc.ResultType.PASS

コード例 #3

ファイル: test_qc.py プロジェクト: STARInformatics/ontobio

def test_gorule30():
    a = ["blah"] * 16
    a[5] = "GO_REF:0000033"

    config = assocparser.AssocParserConfig(
        goref_metadata={
            "goref-0000033": {
                "authors":
                "Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
                "id": "GO_REF:0000033",
                "is_obsolete": True
            }
        })

    test_result = qc.GoRule30().test(a, config)
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "GO_PAINT:0000000"
    test_result = qc.GoRule30().test(a, config)
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "FOO:123|GO_REF:0000033"
    test_result = qc.GoRule30().test(a, config)
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "FOO:123"
    test_result = qc.GoRule30().test(a, config)
    assert test_result.result_type == qc.ResultType.PASS

コード例 #4

ファイル: test_qc.py プロジェクト: geneontology/ontobio

def test_gorule30():
    a = ["blah"] * 16
    a[5] = "GO_REF:0000033"

    test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "GO_PAINT:0000000"
    test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "FOO:123|GO_REF:0000033"
    test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
    assert test_result.result_type == qc.ResultType.ERROR

    a[5] = "FOO:123"
    test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
    assert test_result.result_type == qc.ResultType.PASS