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mathieulemieuxmathieulemieux
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Merge pull request #117 from bcgsc/task/KBDEV-1163-tests-ensembl-protein
Task/kbdev 1163 tests ensembl protein
2 parents 15180c6 + 16195a0 commit 73473c6

6 files changed

Lines changed: 143 additions & 7 deletions

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‎graphkb/genes.py‎

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"""Methods for retrieving gene annotation lists from GraphKB."""
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from typing import Any, Dict, List, Sequence, Set, Tuple, cast
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from . import GraphKBConnection

‎graphkb/match.py‎

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"""
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Functions which return Variants from GraphKB which match some input variant definition
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"""
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from typing import Dict, List, Optional, Set, Union, cast
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from . import GraphKBConnection
@@ -303,9 +304,11 @@ def compare_positional_variants(
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if not positions_overlap(
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cast(BasicPosition, variant["break1Start"]),
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cast(BasicPosition, reference_variant["break1Start"]),
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None
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if "break1End" not in reference_variant
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else cast(BasicPosition, reference_variant["break1End"]),
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(
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None
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if "break1End" not in reference_variant
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else cast(BasicPosition, reference_variant["break1End"])
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),
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):
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return False
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@@ -318,9 +321,11 @@ def compare_positional_variants(
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if not positions_overlap(
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cast(BasicPosition, variant["break2Start"]),
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cast(BasicPosition, reference_variant["break2Start"]),
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None
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if "break2End" not in reference_variant
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else cast(BasicPosition, reference_variant["break2End"]),
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(
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None
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if "break2End" not in reference_variant
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else cast(BasicPosition, reference_variant["break2End"])
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),
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):
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return False
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‎tests/data.py‎

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Array of variants (diplayName and type) that MUST NOT be matching, but not restricted to
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"""
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# Screening structural variant to rule out small events [KBDEV_1056]
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structuralVariants = {
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# Unambiguous structural variations

‎tests/test_genes.py‎

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"""
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Tests here depend on specific data in GraphKB which can change. To avoid this, expected/stable values are chosen
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"""
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import os
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import pytest

‎tests/test_match.py‎

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@@ -79,6 +79,135 @@ def test_checks_by_source_id_kras(self, conn):
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]
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assert "KRAS" in kras
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# KBDEV-1163
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# Testing if the addition of Ensembl protein Features are limiting results
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# returned by get_equivalent_features() since SimilatTo queryType queries
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# aren't traversing the graph to it's whole depth.
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@pytest.mark.skipif(EXCLUDE_INTEGRATION_TESTS, reason="excluding data-specific test")
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def test_ensembl_protein(self, conn):
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for feature, expected in [
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# Sample
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(
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'EGFR',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NM_001346897',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NM_001346897.2',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NP_001333826',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'NP_001333826.1',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648', # Warn: Versionized ENSG won't be returned due to API limitations
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826',
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'NP_001333826.1',
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],
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),
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(
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'ENSG00000146648',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
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],
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),
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(
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'ENSG00000146648.17',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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'NM_001346897',
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'NM_001346897.2',
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'NP_001333826', # Warn: Versionized NP won't be returned due to API limitations
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],
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),
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(
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'ENST00000275493',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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],
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),
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(
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'ENST00000275493.6',
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[
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'EGFR',
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'ERBB',
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'ENSG00000146648',
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'ENSG00000146648.17',
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'ENST00000275493',
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'ENST00000275493.6',
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],
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),
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]:
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equivalent_features = match.get_equivalent_features(conn, feature)
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equivalent_features = [el['displayName'] for el in equivalent_features]
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for equivalent_feature in expected:
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assert equivalent_feature in equivalent_features
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class TestMatchCopyVariant:
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def test_bad_category(self, conn):

‎tests/test_vocab.py‎

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"""
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Tests here depend on specific data in GraphKB which can change. To avoid this, expected/stable values are chosen
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"""
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import os
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import pytest

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