-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add back mutation pattern regression tests
- Loading branch information
1 parent
8dd3cb9
commit cf9ab78
Showing
15 changed files
with
4,793 additions
and
4,981 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 20240113194711 | ||
| 20240121063513 |
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
Submodule hivfacts
updated
9 files
Submodule sierra-core
updated
2 files
| +1 −1 | build.gradle | |
| +28 −20 | src/main/java/edu/stanford/hivdb/genotypes/Genotype.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
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
156 changes: 156 additions & 0 deletions
156
...sts/src/test/java/edu/stanford/hivdb/drugresistance/mutationpattern/MutationPatterns.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 +1,156 @@ | ||
| /* | ||
| Copyright (C) 2024 Stanford HIVDB team | ||
| This file is part of Sierra. | ||
| Sierra is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| Sierra is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with Sierra. If not, see <https://www.gnu.org/licenses/>. | ||
| */ | ||
| package edu.stanford.hivdb.drugresistance.mutationpattern; | ||
|
|
||
| import java.io.IOException; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.ArrayList; | ||
| import java.util.Collections; | ||
|
|
||
| import com.google.gson.reflect.TypeToken; | ||
|
|
||
| import edu.stanford.hivdb.drugresistance.GeneDR; | ||
| import edu.stanford.hivdb.drugresistance.algorithm.ASIDrugSusc; | ||
| import edu.stanford.hivdb.drugresistance.algorithm.DrugResistanceAlgorithm; | ||
| import edu.stanford.hivdb.drugs.Drug; | ||
| import edu.stanford.hivdb.drugs.DrugClass; | ||
| import edu.stanford.hivdb.hivfacts.HIV; | ||
| import edu.stanford.hivdb.mutations.MutationSet; | ||
| import edu.stanford.hivdb.testutils.TestUtils; | ||
| import edu.stanford.hivdb.utilities.Json; | ||
| import edu.stanford.hivdb.viruses.Gene; | ||
| import edu.stanford.hivdb.viruses.Strain; | ||
|
|
||
|
|
||
| public class MutationPatterns { | ||
|
|
||
| private static HIV hiv = HIV.getInstance(); | ||
|
|
||
| public static class MutationPattern { | ||
| public final Gene<HIV> gene; | ||
| public final DrugClass<HIV> drugClass; | ||
| public final MutationSet<HIV> mutations; | ||
| public final Integer count; | ||
| private transient GeneDR<HIV> geneDR = null; | ||
|
|
||
| public MutationPattern( | ||
| Gene<HIV> gene, | ||
| DrugClass<HIV> drugClass, | ||
| MutationSet<HIV> mutations, | ||
| Integer count | ||
| ) { | ||
| this.gene = gene; | ||
| this.drugClass = drugClass; | ||
| this.mutations = mutations; | ||
| this.count = count; | ||
| } | ||
|
|
||
| public GeneDR<HIV> getGeneDR(DrugResistanceAlgorithm<HIV> algorithm) { | ||
| if (geneDR == null) { | ||
| geneDR = new GeneDR<>(gene, mutations, algorithm); | ||
| } | ||
| return geneDR; | ||
| } | ||
|
|
||
| @Override | ||
| public String toString() { | ||
| return String.format( | ||
| "MutationPattern(%s, count=%d, gene=%s, drugClass=%d)", | ||
| mutations.join(), count, gene, drugClass); | ||
| } | ||
| } | ||
|
|
||
| private static Map<DrugClass<HIV>, List<MutationPattern>> allMutationPatterns; | ||
|
|
||
| public static Map<DrugClass<HIV>, List<MutationPattern>> load() throws IOException { | ||
| String resPath = "patterns_hiv1.json"; | ||
| String payload = TestUtils.readTestResourceToString(resPath); | ||
| ArrayList<LinkedHashMap<String, ?>> rawPatterns = Json.loads( | ||
| payload, | ||
| new TypeToken<ArrayList<LinkedHashMap<String, ?>>>(){} | ||
| ); | ||
| LinkedHashMap<DrugClass<HIV>, List<MutationPattern>> patterns = new LinkedHashMap<>(); | ||
| Strain<HIV> hiv1b = hiv.getMainStrain(); | ||
| for (LinkedHashMap<String, ?> rawPattern : rawPatterns) { | ||
| DrugClass<HIV> dc = hiv.getDrugClass((String) rawPattern.get("drug_class")); | ||
| Gene<HIV> gene = hiv1b.getGene(dc.getAbstractGene()); | ||
| Integer count = ((Double) rawPattern.get("count")).intValue(); | ||
| MutationSet<HIV> mutations = MutationSet.parseString( | ||
| gene, | ||
| (String) rawPattern.get("pattern") | ||
| ); | ||
| MutationPattern pattern = new MutationPattern(gene, dc, mutations, count); | ||
| if (!patterns.containsKey(dc)) { | ||
| patterns.put(dc, new ArrayList<>()); | ||
| } | ||
| patterns.get(dc).add(pattern); | ||
| } | ||
| return patterns; | ||
| } | ||
|
|
||
| static { | ||
| try { | ||
| allMutationPatterns = load(); | ||
| } catch (IOException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| private DrugClass<HIV> drugClass; | ||
|
|
||
| /** | ||
| * The tblPatterns<DrugClass> in HIVDB_Scores has the following fields: | ||
| * Pattern, Count, Version, Drug, Level, TotalScore, MutScore, ComboScore, MutScoreText, ComboScoreText | ||
| * The Version should always be the same as the active version used by the program | ||
| * | ||
| * @param drugClass | ||
| */ | ||
| public MutationPatterns(DrugClass<HIV> drugClass) { | ||
| this.drugClass = drugClass; | ||
| } | ||
|
|
||
| public DrugClass<HIV> getDrugClass() { return drugClass; } | ||
|
|
||
| public List<MutationPattern> getPatterns() { | ||
| return allMutationPatterns.getOrDefault(drugClass, Collections.emptyList()); | ||
| } | ||
|
|
||
| public String dumps(DrugResistanceAlgorithm<HIV> algorithm) { | ||
| List<Map<String, ?>> results = new ArrayList<>(); | ||
| for (MutationPattern pattern : getPatterns()) { | ||
| Map<String, Object> result = new LinkedHashMap<>(); | ||
| result.put("gene", pattern.gene.getAbstractGene()); | ||
| result.put("drugClass", pattern.drugClass.getName()); | ||
| result.put("pattern", pattern.mutations.join()); | ||
| result.put("count", pattern.count); | ||
| GeneDR<HIV> geneDR = pattern.getGeneDR(algorithm); | ||
| for(Drug<HIV> drug : pattern.drugClass.getDrugs()) { | ||
| ASIDrugSusc<HIV> susc = geneDR.getDrugSusc(drug); | ||
| result.put(String.format("%s Level", drug.getDisplayAbbr()), susc.getLevel()); | ||
| result.put(String.format("%s Score", drug.getDisplayAbbr()), susc.getScore()); | ||
| } | ||
| results.add(result); | ||
| } | ||
| return Json.dumps(results); | ||
| } | ||
|
|
||
| } |
Oops, something went wrong.