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Merge pull request #2368 from opencb/TASK-5425
TASK-5425 - PortPatch 1.10.1 -> 2.0.0
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53 changes: 53 additions & 0 deletions
53
...lysis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalTsvAnnotationLoader.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * 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. | ||
| */ | ||
|
|
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| package org.opencb.opencga.analysis.clinical; | ||
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| import org.opencb.commons.datastore.core.ObjectMap; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.opencga.analysis.annotations.TsvAnnotationLoader; | ||
| import org.opencb.opencga.catalog.exceptions.CatalogException; | ||
| import org.opencb.opencga.catalog.managers.AnnotationSetManager; | ||
| import org.opencb.opencga.catalog.utils.Constants; | ||
| import org.opencb.opencga.catalog.utils.ParamUtils; | ||
| import org.opencb.opencga.core.models.clinical.ClinicalAnalysisUpdateParams; | ||
| import org.opencb.opencga.core.models.common.AnnotationSet; | ||
| import org.opencb.opencga.core.models.common.Enums; | ||
| import org.opencb.opencga.core.tools.annotations.Tool; | ||
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|
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| import java.util.Collections; | ||
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| @Tool(id = ClinicalTsvAnnotationLoader.ID, resource = Enums.Resource.CLINICAL_ANALYSIS, type = Tool.Type.OPERATION, | ||
| description = "Load annotations from TSV file.") | ||
| public class ClinicalTsvAnnotationLoader extends TsvAnnotationLoader { | ||
| public final static String ID = "clinical-tsv-load"; | ||
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| @Override | ||
| public int count(Query query) throws CatalogException { | ||
| return catalogManager.getClinicalAnalysisManager().count(study, query, token).getNumResults(); | ||
| } | ||
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| @Override | ||
| public void addAnnotationSet(String entryId, AnnotationSet annotationSet, QueryOptions options) throws CatalogException { | ||
| ClinicalAnalysisUpdateParams updateParams = new ClinicalAnalysisUpdateParams() | ||
| .setAnnotationSets(Collections.singletonList(annotationSet)); | ||
| QueryOptions queryOptions = options != null ? new QueryOptions(options) : new QueryOptions(); | ||
| queryOptions.put(Constants.ACTIONS, new ObjectMap(AnnotationSetManager.ANNOTATION_SETS, ParamUtils.BasicUpdateAction.ADD)); | ||
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| catalogManager.getClinicalAnalysisManager().update(study, entryId, updateParams, queryOptions, token); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| --- | ||
| analysisMode: PASS_ONLY | ||
| inheritanceModes: { | ||
| AUTOSOMAL_DOMINANT: 0.1, | ||
| AUTOSOMAL_RECESSIVE_HOM_ALT: 0.1, | ||
| AUTOSOMAL_RECESSIVE_COMP_HET: 2.0, | ||
| X_DOMINANT: 0.1, | ||
| X_RECESSIVE_HOM_ALT: 0.1, | ||
| X_RECESSIVE_COMP_HET: 2.0, | ||
| MITOCHONDRIAL: 0.2 | ||
| } | ||
| frequencySources: [ | ||
| THOUSAND_GENOMES, | ||
| TOPMED, | ||
| UK10K, | ||
|
|
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| ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, | ||
|
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| EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, | ||
| EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN, | ||
| EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, | ||
| EXAC_OTHER, | ||
|
|
||
| GNOMAD_E_AFR, | ||
| GNOMAD_E_AMR, | ||
| # GNOMAD_E_ASJ, | ||
| GNOMAD_E_EAS, | ||
| GNOMAD_E_FIN, | ||
| GNOMAD_E_NFE, | ||
| GNOMAD_E_OTH, | ||
| GNOMAD_E_SAS, | ||
|
|
||
| GNOMAD_G_AFR, | ||
| GNOMAD_G_AMR, | ||
| # GNOMAD_G_ASJ, | ||
| GNOMAD_G_EAS, | ||
| GNOMAD_G_FIN, | ||
| GNOMAD_G_NFE, | ||
| GNOMAD_G_OTH, | ||
| GNOMAD_G_SAS | ||
| ] | ||
| # Possible pathogenicitySources: (POLYPHEN, MUTATION_TASTER, SIFT), (REVEL, MVP), CADD, REMM | ||
| # REMM is trained on non-coding regulatory regions | ||
| # *WARNING* if you enable CADD or REMM ensure that you have downloaded and installed the CADD/REMM tabix files | ||
| # and updated their location in the application.properties. Exomiser will not run without this. | ||
| pathogenicitySources: [ REVEL, MVP ] | ||
| #this is the standard exomiser order. | ||
| steps: [ | ||
| failedVariantFilter: { }, | ||
| variantEffectFilter: { | ||
| remove: [ | ||
| FIVE_PRIME_UTR_EXON_VARIANT, | ||
| FIVE_PRIME_UTR_INTRON_VARIANT, | ||
| THREE_PRIME_UTR_EXON_VARIANT, | ||
| THREE_PRIME_UTR_INTRON_VARIANT, | ||
| NON_CODING_TRANSCRIPT_EXON_VARIANT, | ||
| NON_CODING_TRANSCRIPT_INTRON_VARIANT, | ||
| CODING_TRANSCRIPT_INTRON_VARIANT, | ||
| UPSTREAM_GENE_VARIANT, | ||
| DOWNSTREAM_GENE_VARIANT, | ||
| INTERGENIC_VARIANT, | ||
| REGULATORY_REGION_VARIANT | ||
| ] | ||
| }, | ||
| frequencyFilter: { maxFrequency: 2.0 }, | ||
| pathogenicityFilter: { keepNonPathogenic: true }, | ||
| inheritanceFilter: { }, | ||
| omimPrioritiser: { }, | ||
| hiPhivePrioritiser: { } | ||
| ] |
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