From 7ab8da37af635433b88a7aa573a68b1f9e14f5c4 Mon Sep 17 00:00:00 2001 From: xyg123 Date: Tue, 12 Mar 2024 11:36:29 +0000 Subject: [PATCH 1/4] fix: pytest for coloc unit tests --- tests/gentropy/conftest.py | 44 ++++++++++++++++++ .../method/test_colocalisation_method.py | 45 ++++++++++++------- 2 files changed, 73 insertions(+), 16 deletions(-) diff --git a/tests/gentropy/conftest.py b/tests/gentropy/conftest.py index c7af5a589..674a0f202 100644 --- a/tests/gentropy/conftest.py +++ b/tests/gentropy/conftest.py @@ -2,6 +2,7 @@ from __future__ import annotations from pathlib import Path +from typing import Any import dbldatagen as dg import hail as hl @@ -646,3 +647,46 @@ def sample_data_for_susie_inf() -> list[np.ndarray]: lbf_moments = np.loadtxt("tests/gentropy/data_samples/01_test_lbf_moments.csv") lbf_mle = np.loadtxt("tests/gentropy/data_samples/01_test_lbf_mle.csv") return [ld, z, lbf_moments, lbf_mle] + + +@pytest.fixture() +def sample_data_for_coloc(spark: SparkSession) -> list[Any]: + """Sample data for Coloc tests.""" + overlap_df = spark.read.parquet( + "tests/gentropy/data_samples/coloc_test_data.snappy.parquet" + ) + expected_df = spark.createDataFrame( + [ + { + "h0": 1.3769995397857477e-18, + "h1": 2.937336451601565e-10, + "h2": 8.593226431647826e-12, + "h3": 8.338916748775843e-4, + "h4": 0.9991661080227981, + } + ] + ) + single_snp_coloc = spark.createDataFrame( + [ + { + "leftStudyLocusId": 1, + "rightStudyLocusId": 2, + "chromosome": "1", + "tagVariantId": "snp", + "left_logBF": 10.3, + "right_logBF": 10.5, + } + ] + ) + expected_single_snp_coloc = spark.createDataFrame( + [ + { + "h0": 9.254841951638903e-5, + "h1": 2.7517068829182966e-4, + "h2": 3.3609423764447284e-4, + "h3": 9.254841952564387e-13, + "h4": 0.9992961866536217, + } + ] + ) + return [overlap_df, expected_df, single_snp_coloc, expected_single_snp_coloc] diff --git a/tests/gentropy/method/test_colocalisation_method.py b/tests/gentropy/method/test_colocalisation_method.py index a4fe07646..1f52244be 100644 --- a/tests/gentropy/method/test_colocalisation_method.py +++ b/tests/gentropy/method/test_colocalisation_method.py @@ -2,10 +2,11 @@ from __future__ import annotations +from typing import Any + from gentropy.dataset.colocalisation import Colocalisation from gentropy.dataset.study_locus_overlap import StudyLocusOverlap from gentropy.method.colocalisation import Coloc, ECaviar -from pyspark.sql import SparkSession from pyspark.sql import functions as f @@ -15,27 +16,39 @@ def test_coloc(mock_study_locus_overlap: StudyLocusOverlap) -> None: def test_coloc_colocalise( - spark: SparkSession, - threshold: float = 1e-5, + sample_data_for_coloc: list[Any], + threshold: float = 1e-4, ) -> None: """Compare COLOC results with R implementation, using provided sample dataset from R package (StudyLocusOverlap).""" - test_overlap_df = spark.read.parquet( - "tests/gentropy/data_samples/coloc_test_data.snappy.parquet", header=True + test_overlap_df = sample_data_for_coloc[0] + test_overlap = StudyLocusOverlap( + _df=test_overlap_df, _schema=StudyLocusOverlap.get_schema() ) - test_overlap = StudyLocusOverlap(test_overlap_df, StudyLocusOverlap.get_schema()) test_result = Coloc.colocalise(test_overlap) + expected = sample_data_for_coloc[1] + difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) + for col in difference.columns: + assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 - expected = spark.createDataFrame( - [ - { - "h0": 1.3769995397857477e-18, - "h1": 2.937336451601565e-10, - "h2": 8.593226431647826e-12, - "h3": 8.338916748775843e-4, - "h4": 0.9991661080227981, - } - ] + +def test_single_snp_coloc( + sample_data_for_coloc: list[Any], + threshold: float = 1e-5, +) -> None: + """Test edge case of coloc where only one causal SNP is present in the StudyLocusOverlap.""" + test_overlap_df = sample_data_for_coloc[2] + test_overlap = StudyLocusOverlap( + _df=test_overlap_df.select( + "leftStudyLocusId", + "rightStudyLocusId", + "chromosome", + "tagVariantId", + f.struct(f.col("left_logBF"), f.col("right_logBF")).alias("statistics"), + ), + _schema=StudyLocusOverlap.get_schema(), ) + test_result = Coloc.colocalise(test_overlap) + expected = sample_data_for_coloc[3] difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) for col in difference.columns: assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 From 8aa507d2892183402e9b4fb41bd3f879e0ded6b9 Mon Sep 17 00:00:00 2001 From: xyg123 Date: Tue, 12 Mar 2024 12:32:55 +0000 Subject: [PATCH 2/4] fix: removed unused coloc tests --- .../method/test_colocalisation_method.py | 134 ------------------ 1 file changed, 134 deletions(-) diff --git a/tests/gentropy/method/test_colocalisation_method.py b/tests/gentropy/method/test_colocalisation_method.py index f28ddf120..1f52244be 100644 --- a/tests/gentropy/method/test_colocalisation_method.py +++ b/tests/gentropy/method/test_colocalisation_method.py @@ -54,140 +54,6 @@ def test_single_snp_coloc( assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 -def test_single_snp_coloc( - spark: SparkSession, - threshold: float = 1e-5, -) -> None: - """Test edge case of coloc where only one causal SNP is present in the StudyLocusOverlap.""" - test_overlap_df = spark.createDataFrame( - [ - { - "leftStudyLocusId": 1, - "rightStudyLocusId": 2, - "chromosome": "1", - "tagVariantId": "snp", - "left_logBF": 10.3, - "right_logBF": 10.5, - } - ] - ) - test_overlap = StudyLocusOverlap( - test_overlap_df.select( - "leftStudyLocusId", - "rightStudyLocusId", - "chromosome", - "tagVariantId", - f.struct(f.col("left_logBF"), f.col("right_logBF")).alias("statistics"), - ), - StudyLocusOverlap.get_schema(), - ) - test_result = Coloc.colocalise(test_overlap) - - expected = spark.createDataFrame( - [ - { - "h0": 9.254841951638903e-5, - "h1": 2.7517068829182966e-4, - "h2": 3.3609423764447284e-4, - "h3": 9.254841952564387e-13, - "h4": 0.9992961866536217, - } - ] - ) - difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) - for col in difference.columns: - assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 - - -def test_single_snp_coloc_one_negative( - spark: SparkSession, - threshold: float = 1e-5, -) -> None: - """Test edge case of coloc where only one causal SNP is present (On one side!) in the StudyLocusOverlap.""" - test_overlap_df = spark.createDataFrame( - [ - { - "leftStudyLocusId": 1, - "rightStudyLocusId": 2, - "chromosome": "1", - "tagVariantId": "snp", - "left_logBF": 18.3, - "right_logBF": 0.01, - } - ] - ) - test_overlap = StudyLocusOverlap( - test_overlap_df.select( - "leftStudyLocusId", - "rightStudyLocusId", - "chromosome", - "tagVariantId", - f.struct(f.col("left_logBF"), f.col("right_logBF")).alias("statistics"), - ), - StudyLocusOverlap.get_schema(), - ) - test_result = Coloc.colocalise(test_overlap) - test_result.df.show(1, False) - expected = spark.createDataFrame( - [ - { - "h0": 1.0246538505087709e-4, - "h1": 0.9081680002273896, - "h2": 1.0349517929098209e-8, - "h3": 1.0246538506112363e-12, - "h4": 0.09172952403701702, - } - ] - ) - difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) - for col in difference.columns: - assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 - - -def test_single_snp_coloc_both_negative( - spark: SparkSession, - threshold: float = 1e-5, -) -> None: - """Test edge case of coloc where only one non-causal SNP overlaps in the StudyLocusOverlap.""" - test_overlap_df = spark.createDataFrame( - [ - { - "leftStudyLocusId": 1, - "rightStudyLocusId": 2, - "chromosome": "1", - "tagVariantId": "snp", - "left_logBF": 0.03, - "right_logBF": 0.01, - } - ] - ) - test_overlap = StudyLocusOverlap( - test_overlap_df.select( - "leftStudyLocusId", - "rightStudyLocusId", - "chromosome", - "tagVariantId", - f.struct(f.col("left_logBF"), f.col("right_logBF")).alias("statistics"), - ), - StudyLocusOverlap.get_schema(), - ) - test_result = Coloc.colocalise(test_overlap) - expected = spark.createDataFrame( - [ - { - "h0": 0.9997855774090624, - "h1": 1.0302335812225042e-4, - "h2": 1.0098335895103664e-4, - "h3": 9.9978557750904e-9, - "h4": 1.0405876008495098e-5, - } - ] - ) - difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) - for col in difference.columns: - assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 - - def test_ecaviar(mock_study_locus_overlap: StudyLocusOverlap) -> None: """Test eCAVIAR.""" assert isinstance(ECaviar.colocalise(mock_study_locus_overlap), Colocalisation) From 5e58c4f351995a1d66f06af3ec136a8512754891 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Wed, 13 Mar 2024 09:41:18 +0000 Subject: [PATCH 3/4] test(coloc): add coloc semantic test (#538) * test(coloc): define fixtures and parametrise coloc tests * test(coloc): compare dfs with assert_frame_equal --- tests/gentropy/conftest.py | 44 ------- .../coloc_test_data.snappy.parquet | Bin 11927 -> 0 bytes .../method/test_colocalisation_method.py | 119 +++++++++++++----- 3 files changed, 85 insertions(+), 78 deletions(-) delete mode 100644 tests/gentropy/data_samples/coloc_test_data.snappy.parquet diff --git a/tests/gentropy/conftest.py b/tests/gentropy/conftest.py index 13992f8f2..78bd567da 100644 --- a/tests/gentropy/conftest.py +++ b/tests/gentropy/conftest.py @@ -3,7 +3,6 @@ from __future__ import annotations from pathlib import Path -from typing import Any import dbldatagen as dg import hail as hl @@ -648,46 +647,3 @@ def sample_data_for_susie_inf() -> list[np.ndarray]: lbf_moments = np.loadtxt("tests/gentropy/data_samples/01_test_lbf_moments.csv") lbf_mle = np.loadtxt("tests/gentropy/data_samples/01_test_lbf_mle.csv") return [ld, z, lbf_moments, lbf_mle] - - -@pytest.fixture() -def sample_data_for_coloc(spark: SparkSession) -> list[Any]: - """Sample data for Coloc tests.""" - overlap_df = spark.read.parquet( - "tests/gentropy/data_samples/coloc_test_data.snappy.parquet" - ) - expected_df = spark.createDataFrame( - [ - { - "h0": 1.3769995397857477e-18, - "h1": 2.937336451601565e-10, - "h2": 8.593226431647826e-12, - "h3": 8.338916748775843e-4, - "h4": 0.9991661080227981, - } - ] - ) - single_snp_coloc = spark.createDataFrame( - [ - { - "leftStudyLocusId": 1, - "rightStudyLocusId": 2, - "chromosome": "1", - "tagVariantId": "snp", - "left_logBF": 10.3, - "right_logBF": 10.5, - } - ] - ) - expected_single_snp_coloc = spark.createDataFrame( - [ - { - "h0": 9.254841951638903e-5, - "h1": 2.7517068829182966e-4, - "h2": 3.3609423764447284e-4, - "h3": 9.254841952564387e-13, - "h4": 0.9992961866536217, - } - ] - ) - return [overlap_df, expected_df, single_snp_coloc, expected_single_snp_coloc] diff --git 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b/tests/gentropy/method/test_colocalisation_method.py index 1f52244be..d311d88ad 100644 --- a/tests/gentropy/method/test_colocalisation_method.py +++ b/tests/gentropy/method/test_colocalisation_method.py @@ -4,10 +4,12 @@ from typing import Any +import pytest from gentropy.dataset.colocalisation import Colocalisation from gentropy.dataset.study_locus_overlap import StudyLocusOverlap from gentropy.method.colocalisation import Coloc, ECaviar -from pyspark.sql import functions as f +from pandas.testing import assert_frame_equal +from pyspark.sql import SparkSession def test_coloc(mock_study_locus_overlap: StudyLocusOverlap) -> None: @@ -15,43 +17,92 @@ def test_coloc(mock_study_locus_overlap: StudyLocusOverlap) -> None: assert isinstance(Coloc.colocalise(mock_study_locus_overlap), Colocalisation) -def test_coloc_colocalise( - sample_data_for_coloc: list[Any], - threshold: float = 1e-4, -) -> None: - """Compare COLOC results with R implementation, using provided sample dataset from R package (StudyLocusOverlap).""" - test_overlap_df = sample_data_for_coloc[0] - test_overlap = StudyLocusOverlap( - _df=test_overlap_df, _schema=StudyLocusOverlap.get_schema() - ) - test_result = Coloc.colocalise(test_overlap) - expected = sample_data_for_coloc[1] - difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) - for col in difference.columns: - assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 - - -def test_single_snp_coloc( - sample_data_for_coloc: list[Any], +@pytest.mark.parametrize( + "observed_data, expected_data", + [ + # associations with a single overlapping SNP + ( + # observed overlap + [ + { + "leftStudyLocusId": 1, + "rightStudyLocusId": 2, + "chromosome": "1", + "tagVariantId": "snp", + "statistics": {"left_logBF": 10.3, "right_logBF": 10.5}, + }, + ], + # expected coloc + [ + { + "h0": 9.254841951638903e-5, + "h1": 2.7517068829182966e-4, + "h2": 3.3609423764447284e-4, + "h3": 9.254841952564387e-13, + "h4": 0.9992961866536217, + }, + ], + ), + # associations with multiple overlapping SNPs + ( + # observed overlap + [ + { + "leftStudyLocusId": 1, + "rightStudyLocusId": 2, + "chromosome": "1", + "tagVariantId": "snp1", + "statistics": {"left_logBF": 10.3, "right_logBF": 10.5}, + }, + { + "leftStudyLocusId": 1, + "rightStudyLocusId": 2, + "chromosome": "1", + "tagVariantId": "snp2", + "statistics": {"left_logBF": 10.3, "right_logBF": 10.5}, + }, + ], + # expected coloc + [ + { + "h0": 4.6230151407950416e-5, + "h1": 2.749086942648107e-4, + "h2": 3.357742374172504e-4, + "h3": 9.983447421747411e-4, + "h4": 0.9983447421747356, + }, + ], + ), + ], +) +def test_coloc_semantic( + spark: SparkSession, + observed_data: list[Any], + expected_data: list[Any], threshold: float = 1e-5, ) -> None: - """Test edge case of coloc where only one causal SNP is present in the StudyLocusOverlap.""" - test_overlap_df = sample_data_for_coloc[2] - test_overlap = StudyLocusOverlap( - _df=test_overlap_df.select( - "leftStudyLocusId", - "rightStudyLocusId", - "chromosome", - "tagVariantId", - f.struct(f.col("left_logBF"), f.col("right_logBF")).alias("statistics"), - ), + """Test our COLOC with the implementation in R.""" + observed_overlap = StudyLocusOverlap( + _df=spark.createDataFrame(observed_data, schema=StudyLocusOverlap.get_schema()), _schema=StudyLocusOverlap.get_schema(), ) - test_result = Coloc.colocalise(test_overlap) - expected = sample_data_for_coloc[3] - difference = test_result.df.select("h0", "h1", "h2", "h3", "h4").subtract(expected) - for col in difference.columns: - assert difference.filter(f.abs(f.col(col)) > threshold).count() == 0 + observed_coloc_pdf = ( + Coloc.colocalise(observed_overlap) + .df.select("h0", "h1", "h2", "h3", "h4") + .toPandas() + ) + expected_coloc_pdf = ( + spark.createDataFrame(expected_data) + .select("h0", "h1", "h2", "h3", "h4") + .toPandas() + ) + + assert_frame_equal( + observed_coloc_pdf, + expected_coloc_pdf, + check_exact=False, + check_dtype=True, + ) def test_ecaviar(mock_study_locus_overlap: StudyLocusOverlap) -> None: From a6ad0c462a5c7d1ade542078c7efba01c1dc872e Mon Sep 17 00:00:00 2001 From: xyg123 Date: Wed, 20 Mar 2024 11:09:21 +0000 Subject: [PATCH 4/4] fix: remove unused threshold variable --- tests/gentropy/method/test_colocalisation_method.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/gentropy/method/test_colocalisation_method.py b/tests/gentropy/method/test_colocalisation_method.py index d311d88ad..37613354c 100644 --- a/tests/gentropy/method/test_colocalisation_method.py +++ b/tests/gentropy/method/test_colocalisation_method.py @@ -79,7 +79,6 @@ def test_coloc_semantic( spark: SparkSession, observed_data: list[Any], expected_data: list[Any], - threshold: float = 1e-5, ) -> None: """Test our COLOC with the implementation in R.""" observed_overlap = StudyLocusOverlap(