-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
update/fix variant stat calculation (#198)
* update variant stat calculation
- Loading branch information
Showing
5 changed files
with
212 additions
and
9 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
183 changes: 183 additions & 0 deletions
183
.../configuration/jobs/steps/variantstats/VariantStatsStepTestWithMultipleEntriesForFid.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,183 @@ | ||
| /* | ||
| * Copyright 2024 EMBL - European Bioinformatics Institute | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package uk.ac.ebi.eva.pipeline.configuration.jobs.steps.variantstats; | ||
|
|
||
| import com.mongodb.client.MongoCollection; | ||
| import org.bson.Document; | ||
| import org.junit.After; | ||
| import org.junit.Assert; | ||
| import org.junit.Before; | ||
| import org.junit.Rule; | ||
| import org.junit.Test; | ||
| import org.junit.runner.RunWith; | ||
| import org.springframework.batch.core.JobExecution; | ||
| import org.springframework.batch.core.JobParameters; | ||
| import org.springframework.batch.test.JobLauncherTestUtils; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.test.context.ContextConfiguration; | ||
| import org.springframework.test.context.TestPropertySource; | ||
| import org.springframework.test.context.junit4.SpringRunner; | ||
| import uk.ac.ebi.eva.pipeline.configuration.BeanNames; | ||
| import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; | ||
| import uk.ac.ebi.eva.pipeline.configuration.jobs.VariantStatsJobConfiguration; | ||
| import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.VariantStatsStepConfiguration; | ||
| import uk.ac.ebi.eva.test.configuration.BatchTestConfiguration; | ||
| import uk.ac.ebi.eva.test.configuration.TemporaryRuleConfiguration; | ||
| import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; | ||
| import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; | ||
| import uk.ac.ebi.eva.utils.EvaJobParameterBuilder; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
||
| import static org.junit.Assert.assertEquals; | ||
| import static uk.ac.ebi.eva.test.utils.JobTestUtils.assertCompleted; | ||
|
|
||
| /** | ||
| * Test for {@link VariantStatsStepConfiguration} | ||
| */ | ||
| @RunWith(SpringRunner.class) | ||
| @TestPropertySource({"classpath:test-stats.properties"}) | ||
| @ContextConfiguration(classes = {VariantStatsJobConfiguration.class, BatchTestConfiguration.class, | ||
| TemporaryRuleConfiguration.class, MongoConfiguration.class}) | ||
| public class VariantStatsStepTestWithMultipleEntriesForFid { | ||
| private static final String COLLECTION_VARIANTS_NAME = "variants"; | ||
|
|
||
| private static final String COLLECTION_FILES_NAME = "files"; | ||
|
|
||
| private static final String DATABASE_NAME = "variant_stats_test_db"; | ||
|
|
||
| @Autowired | ||
| @Rule | ||
| public TemporaryMongoRule mongoRule; | ||
|
|
||
| @Rule | ||
| public PipelineTemporaryFolderRule temporaryFolderRule = new PipelineTemporaryFolderRule(); | ||
|
|
||
| @Autowired | ||
| private JobLauncherTestUtils jobLauncherTestUtils; | ||
|
|
||
| @Before | ||
| public void setUp() throws Exception { | ||
| mongoRule.getTemporaryDatabase(DATABASE_NAME).drop(); | ||
| } | ||
|
|
||
| @After | ||
| public void cleanUp() { | ||
| mongoRule.getTemporaryDatabase(DATABASE_NAME).drop(); | ||
| } | ||
|
|
||
| @Test | ||
| public void variantStatsStepShouldCalculateAndLoadStats_WhereFidHasMoreThanOneFile() { | ||
| MongoCollection<Document> filesCollection = mongoRule.getCollection(DATABASE_NAME, COLLECTION_FILES_NAME); | ||
| MongoCollection<Document> variantsCollection = mongoRule.getCollection(DATABASE_NAME, COLLECTION_VARIANTS_NAME); | ||
|
|
||
| filesCollection.insertMany(Arrays.asList( | ||
| new Document("sid", "sid1").append("fid", "fid1").append("fname", "fname11") | ||
| .append("samp", new Document("samp11", 0).append("samp12", 1).append("samp13", 2)), | ||
| // multiple entries for fid2 in the files collection | ||
| new Document("sid", "sid1").append("fid", "fid2").append("fname", "fname21") | ||
| .append("samp", new Document("samp21", 0).append("samp22", 1)).append("samp23", 2), | ||
| new Document("sid", "sid1").append("fid", "fid2").append("fname", "fname22") | ||
| .append("samp", new Document("samp31", 0).append("samp32", 1)).append("samp33", 2) | ||
| )); | ||
|
|
||
| variantsCollection.insertMany(Arrays.asList( | ||
| new Document("_id", "chr1_11111111_A_G").append("ref", "A").append("alt", "G") | ||
| .append("files", Arrays.asList( | ||
| // stats should be calculated | ||
| new Document("sid", "sid1").append("fid", "fid1") | ||
| .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))), | ||
| // should not calculate stats - fid2 has more than one entry in the files collection | ||
| new Document("sid", "sid1").append("fid", "fid2") | ||
| .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))), | ||
| // should not calculate stats - no entry for fid3 in files collection | ||
| new Document("sid", "sid1").append("fid", "fid3") | ||
| .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))), | ||
| // should not calculate stats - different study | ||
| new Document("sid", "sid2").append("fid", "fid1") | ||
| .append("samp", new Document("def", "0|0").append("0|1", Arrays.asList(1))) | ||
| )) | ||
| .append("st", Arrays.asList( | ||
| // should be updated with new values | ||
| new Document("sid", "sid1").append("fid", "fid1") | ||
| .append("maf", 0.1).append("mgf", 0.1) | ||
| .append("mafAl", "A").append("mgfGt", "0|0"), | ||
| // should not change as it belongs to different study id | ||
| new Document("sid", "sid2").append("fid", "fid1") | ||
| .append("maf", 0.20000000298023224).append("mgf", 0.20000000298023224) | ||
| .append("mafAl", "A").append("mgfGt", "0|0"), | ||
| // should not change as it belongs to different fid | ||
| new Document("sid", "sid1").append("fid", "fid3") | ||
| .append("maf", 0.30000001192092896).append("mgf", 0.30000001192092896) | ||
| .append("mafAl", "A").append("mgfGt", "0|0") | ||
|
|
||
| )) | ||
| )); | ||
|
|
||
| JobParameters jobParameters = new EvaJobParameterBuilder() | ||
| .collectionFilesName(COLLECTION_FILES_NAME) | ||
| .collectionVariantsName(COLLECTION_VARIANTS_NAME) | ||
| .databaseName(DATABASE_NAME) | ||
| .inputStudyId("sid1") | ||
| .chunkSize("100") | ||
| .toJobParameters(); | ||
|
|
||
| JobExecution jobExecution = jobLauncherTestUtils.launchStep(BeanNames.VARIANT_STATS_STEP, jobParameters); | ||
|
|
||
| // check job completed successfully | ||
| assertCompleted(jobExecution); | ||
| List<Document> documents = mongoRule.getTemporaryDatabase(DATABASE_NAME).getCollection(COLLECTION_VARIANTS_NAME) | ||
| .find().into(new ArrayList<>()); | ||
| Assert.assertTrue(documents.size() == 1); | ||
|
|
||
| // assert data | ||
| ArrayList<Document> variantStatsList = documents.stream().filter(doc -> doc.get("_id").equals("chr1_11111111_A_G")) | ||
| .findFirst().get().get("st", ArrayList.class); | ||
| assertEquals(3, variantStatsList.size()); | ||
|
|
||
| // assert remained unchanged | ||
| Document variantStatsForSid2Fid1 = variantStatsList.stream() | ||
| .filter(st -> st.get("sid").equals("sid2") && st.get("fid").equals("fid1")).findFirst().get(); | ||
| assertEquals(0.20000000298023224, variantStatsForSid2Fid1.get("maf")); | ||
| assertEquals(0.20000000298023224, variantStatsForSid2Fid1.get("mgf")); | ||
| assertEquals("A", variantStatsForSid2Fid1.get("mafAl")); | ||
| assertEquals("0|0", variantStatsForSid2Fid1.get("mgfGt")); | ||
|
|
||
| // assert remained unchanged | ||
| Document variantStatsForSid1Fid3 = variantStatsList.stream() | ||
| .filter(st -> st.get("sid").equals("sid1") && st.get("fid").equals("fid3")).findFirst().get(); | ||
| assertEquals(0.30000001192092896, variantStatsForSid1Fid3.get("maf")); | ||
| assertEquals(0.30000001192092896, variantStatsForSid1Fid3.get("mgf")); | ||
| assertEquals("A", variantStatsForSid1Fid3.get("mafAl")); | ||
| assertEquals("0|0", variantStatsForSid1Fid3.get("mgfGt")); | ||
|
|
||
| // assert updated with new stats | ||
| Document variantStatsForSid1Fid1 = variantStatsList.stream() | ||
| .filter(st -> st.get("sid").equals("sid1") && st.get("fid").equals("fid1")).findFirst().get(); | ||
| Document numOfGT = (Document) variantStatsForSid1Fid1.get("numGt"); | ||
| assertEquals(2, numOfGT.get("0|0")); | ||
| assertEquals(1, numOfGT.get("0|1")); | ||
| assertEquals(0.1666666716337204, variantStatsForSid1Fid1.get("maf")); | ||
| assertEquals(0.3333333432674408, variantStatsForSid1Fid1.get("mgf")); | ||
| assertEquals("G", variantStatsForSid1Fid1.get("mafAl")); | ||
| assertEquals("0|1", variantStatsForSid1Fid1.get("mgfGt")); | ||
| assertEquals(0, variantStatsForSid1Fid1.get("missAl")); | ||
| assertEquals(0, variantStatsForSid1Fid1.get("missGt")); | ||
| } | ||
|
|
||
| } |