-
Notifications
You must be signed in to change notification settings - Fork 6
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Restricting getTopVariants to top k, adding variantstore support
- Loading branch information
Showing
13 changed files
with
296 additions
and
37 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
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
63 changes: 63 additions & 0 deletions
63
...rity-data-impl/src/main/java/org/phenotips/data/similarity/internal/GAVariantVariant.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 +1,63 @@ | ||
| /* | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership. | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program 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 Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see http://www.gnu.org/licenses/ | ||
| */ | ||
| package org.phenotips.data.similarity.internal; | ||
|
|
||
| import org.phenotips.variantstore.shared.GACallInfoFields; | ||
| import org.phenotips.variantstore.shared.GAVariantInfoFields; | ||
| import org.phenotips.variantstore.shared.VariantUtils; | ||
|
|
||
| import java.util.List; | ||
|
|
||
| import org.apache.commons.lang.StringUtils; | ||
| import org.ga4gh.GACall; | ||
| import org.ga4gh.GAVariant; | ||
|
|
||
| /** | ||
| * A variant from the variant store. Annotated by Exomiser. | ||
| * | ||
| * @version $Id$ | ||
| */ | ||
| public class GAVariantVariant extends AbstractVariant | ||
| { | ||
| /** | ||
| * Create a {@link Variant} from a {@link GAVariant} returned by a {@link | ||
| * org.phenotips.variantstore.VariantStoreInterface}. | ||
| * | ||
| * @param gaVariant a {@link GAVariant} | ||
| */ | ||
| public GAVariantVariant(GAVariant gaVariant) { | ||
| setChrom(gaVariant.getReferenceName()); | ||
| setPosition((int) (gaVariant.getStart() + 1)); | ||
|
|
||
| GACall call = gaVariant.getCalls().get(0); | ||
| List<Integer> genotype = call.getGenotype(); | ||
|
|
||
| setGenotype(gaVariant.getReferenceBases(), | ||
| StringUtils.join(gaVariant.getAlternateBases(), ','), | ||
| StringUtils.join(genotype, '/')); | ||
|
|
||
| setEffect(VariantUtils.getInfo(gaVariant, GAVariantInfoFields.GENE_EFFECT)); | ||
|
|
||
| Object value = VariantUtils.getInfo(call, GACallInfoFields.EXOMISER_VARIANT_SCORE); | ||
| if (value == null || value.equals("null")) { | ||
| setScore(0D); | ||
| } else { | ||
| setScore(Double.valueOf((String) value)); | ||
| } | ||
| } | ||
| } |
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
138 changes: 138 additions & 0 deletions
138
...ity-data-impl/src/main/java/org/phenotips/data/similarity/internal/VariantstoreExome.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 +1,138 @@ | ||
| /* | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership. | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program 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 Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see http://www.gnu.org/licenses/ | ||
| */ | ||
| package org.phenotips.data.similarity.internal; | ||
|
|
||
| import org.phenotips.data.Patient; | ||
| import org.phenotips.data.similarity.Exome; | ||
| import org.phenotips.data.similarity.Variant; | ||
| import org.phenotips.variantStoreIntegration.VariantStoreService; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
|
|
||
| import org.ga4gh.GAVariant; | ||
| import org.json.JSONArray; | ||
|
|
||
| /** | ||
| * An exome implementation that's backed by {{@link VariantStore}}. | ||
| * | ||
| * @version $Id$ | ||
| */ | ||
| public class VariantstoreExome implements Exome | ||
| { | ||
| private final Patient patient; | ||
|
|
||
| private VariantStoreService vs; | ||
|
|
||
| /** | ||
| * Initialize the exome with the variant store and the patient. | ||
| * | ||
| * @param vs the Variant Store instance | ||
| * @param p the patient | ||
| */ | ||
| public VariantstoreExome(VariantStoreService vs, Patient p) { | ||
| this.vs = vs; | ||
| this.patient = p; | ||
| } | ||
|
|
||
| /** | ||
| * Get the names of all genes with variants in the patient. | ||
| * | ||
| * @return an unmodifiable set of gene names with variants in the patient | ||
| */ | ||
| @Override | ||
| public Set<String> getGenes() { | ||
| return vs.getAllGenesForIndividual(patient.getId()); | ||
| } | ||
|
|
||
| /** | ||
| * Return the score for a gene. | ||
| * | ||
| * @param gene the gene in question | ||
| * | ||
| * @return the score of the gene, between 0 and 1, where 1 is better (or | ||
| * {@code null} if no variants for gene) | ||
| */ | ||
| @Override | ||
| public Double getGeneScore(String gene) { | ||
| return vs.getGeneScore(patient.getId(), gene); | ||
| } | ||
|
|
||
| /** | ||
| * Get {@link Variant}s for a gene. | ||
| * | ||
| * @param gene the gene to get {@link Variant}s for. | ||
| * @param k | ||
| * | ||
| * @return an unmodifiable (potentially-empty) list of top {@link Variant}s | ||
| * for the gene, by decreasing score | ||
| */ | ||
| @Override | ||
| public List<Variant> getTopVariants(String gene, int k) { | ||
| List<GAVariant> gaVariants = vs.getTopHarmfullVariantsForGene(patient.getId(), gene, k); | ||
| List<Variant> variants = new ArrayList<>(); | ||
| for (GAVariant gaVariant : gaVariants) { | ||
| variants.add(new GAVariantVariant(gaVariant)); | ||
| } | ||
| return variants; | ||
| } | ||
|
|
||
| /** | ||
| * Get the n highest genes, in descending order of score. If there are fewer | ||
| * than n genes, all will be returned. | ||
| * | ||
| * @param n the number of genes to return (specify 0 for all) | ||
| * | ||
| * @return an unmodifiable (potentially-empty) list of gene names | ||
| */ | ||
| @Override | ||
| public List<String> getTopGenes(int n) { | ||
| return vs.getTopGenesForIndividual(patient.getId(), n); | ||
| } | ||
|
|
||
| /** | ||
| * Retrieve all variant information in a JSON format. For example: | ||
| * <p/> | ||
| * <pre> | ||
| * [ | ||
| * { | ||
| * "gene": "SRCAP", | ||
| * "score": 0.7, // phenotype score | ||
| * "variants": [ // variants sorted by decreasing score | ||
| * { | ||
| * "score": 0.8, // genotype score | ||
| * "chrom": "1", | ||
| * "position": 2014819, | ||
| * "type": "SPLICING", | ||
| * "ref": "A", | ||
| * "alt": "T", | ||
| * }, | ||
| * {...}, | ||
| * ] | ||
| * } | ||
| * ] | ||
| * </pre> | ||
| * | ||
| * @return the data about this value, using the org.json classes | ||
| */ | ||
| @Override | ||
| public JSONArray toJSON() { | ||
| return null; | ||
| } | ||
| } |
Oops, something went wrong.