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...lysis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalTsvAnnotationLoader.java
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/* | ||
* 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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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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--- | ||
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, | ||
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GNOMAD_E_AFR, | ||
GNOMAD_E_AMR, | ||
# GNOMAD_E_ASJ, | ||
GNOMAD_E_EAS, | ||
GNOMAD_E_FIN, | ||
GNOMAD_E_NFE, | ||
GNOMAD_E_OTH, | ||
GNOMAD_E_SAS, | ||
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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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