-
Notifications
You must be signed in to change notification settings - Fork 53
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
lib: some improvements in downloading dbSNP data, #TASK-5816, #TASK-5789
- Loading branch information
Showing
3 changed files
with
197 additions
and
126 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
174 changes: 174 additions & 0 deletions
174
cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/DbSnpBuilder.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 +1,174 @@ | ||
| /* | ||
| * 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. | ||
| */ | ||
|
|
||
| package org.opencb.cellbase.lib.builders; | ||
|
|
||
| import org.opencb.biodata.models.core.Snp; | ||
| import org.opencb.biodata.models.core.SnpAnnotation; | ||
| import org.opencb.biodata.models.variant.avro.PopulationFrequency; | ||
| import org.opencb.cellbase.core.config.DownloadProperties; | ||
| import org.opencb.cellbase.core.serializer.CellBaseFileSerializer; | ||
| import org.opencb.cellbase.core.serializer.CellBaseSerializer; | ||
| import org.opencb.commons.utils.FileUtils; | ||
| import org.slf4j.LoggerFactory; | ||
|
|
||
| import java.io.BufferedReader; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
||
| import static org.opencb.cellbase.lib.EtlCommons.DBSNP_NAME; | ||
|
|
||
| /** | ||
| * Created by imedina on 06/11/15. | ||
| */ | ||
| public class DbSnpBuilder extends CellBaseBuilder { | ||
|
|
||
| private Path sourceVariationPath; | ||
| private DownloadProperties.URLProperties dbSnpUrlProperties; | ||
|
|
||
| public DbSnpBuilder(Path sourceVariationPath, DownloadProperties.URLProperties dbSnpUrlProperties, CellBaseSerializer serializer) { | ||
| super(serializer); | ||
| this.sourceVariationPath = sourceVariationPath; | ||
| this.dbSnpUrlProperties = dbSnpUrlProperties; | ||
|
|
||
| logger = LoggerFactory.getLogger(DbSnpBuilder.class); | ||
| } | ||
|
|
||
| /* Example: | ||
| ## dbSNP 156 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO | ||
| NC_000001.11 926003 rs1329301928 C A,T . . RS=1329301928;dbSNPBuildID=151;SSR=0; | ||
| GENEINFO=SAMD11:148398|LOC107985728:107985728;VC=SNV;NSM;R5;GNO; | ||
| FREQ=Estonian:0.9998,0.0002232,.|TOMMO:0.9999,.,0.0001062|dbGaP_PopFreq:0.9999,5.4e-05,0; | ||
| CLNVI=.,.,;CLNORIGIN=.,.,1;CLNSIG=.,.,0;CLNDISDB=.,.,MedGen:CN517202;CLNDN=.,.,not_provided;CLNREVSTAT=.,.,single; | ||
| CLNACC=.,.,RCV001929748.1;CLNHGVS=NC_000001.11:g.926003=,NC_000001.11:g.926003C>A,NC_000001.11:g.926003C>T | ||
| NC_000001.11 925952 rs1640863258 G A . . RS=1640863258;SSR=0; | ||
| GENEINFO=SAMD11:148398|LOC107985728:107985728;VC=SNV;NSM;R5;CLNVI=.,;CLNORIGIN=.,1;CLNSIG=.,0;CLNDISDB=.,MedGen:CN517202; | ||
| CLNDN=.,not_provided;CLNREVSTAT=.,single;CLNACC=.,RCV001318826.4;CLNHGVS=NC_000001.11:g.925952=,NC_000001.11:g.925952G>A | ||
| NC_000001.11 925953 rs1349221494 G A,T . . RS=1349221494;dbSNPBuildID=151;SSR=0; | ||
| GENEINFO=SAMD11:148398|LOC107985728:107985728;VC=SNV;SYN;R5;GNO; | ||
| FREQ=GnomAD:1,1.426e-05,.|GnomAD_exomes:1,.,4.008e-06|TOPMED:1,3.778e-06,.|dbGaP_PopFreq:1,0,3.124e-05 | ||
| NC_000001.11 925956 rs1342334044 C T . . RS=1342334044;dbSNPBuildID=155;SSR=0; | ||
| GENEINFO=SAMD11:148398|LOC107985728:107985728;VC=SNV;SYN;R5;GNO; | ||
| FREQ=TOPMED:1,1.133e-05|dbGaP_PopFreq:1,0; | ||
| CLNVI=.,;CLNORIGIN=.,1;CLNSIG=.,3;CLNDISDB=.,MedGen:CN517202;CLNDN=.,not_provided;CLNREVSTAT=.,single;CLNACC=.,RCV002170030.3; | ||
| CLNHGVS=NC_000001.11:g.925956=,NC_000001.11:g.925956C>T | ||
| */ | ||
| @Override | ||
| public void parse() throws Exception { | ||
| Path dbSnpFilePath = sourceVariationPath.resolve(Paths.get(dbSnpUrlProperties.getHost()).getFileName()); | ||
| FileUtils.checkPath(dbSnpFilePath); | ||
|
|
||
| CellBaseFileSerializer fileSerializer = (CellBaseFileSerializer) serializer; | ||
|
|
||
| String line; | ||
| String[] fields; | ||
|
|
||
| String currentChromosome = null; | ||
| String chromosome = null; | ||
| int position; | ||
| String id; | ||
| String ref; | ||
| String[] alt; | ||
| String info; | ||
| List<String> flags; | ||
|
|
||
| try (BufferedReader bufferedReader = FileUtils.newBufferedReader(dbSnpFilePath)) { | ||
| while ((line = bufferedReader.readLine()) != null) { | ||
| if (!line.startsWith("#")) { | ||
| fields = line.split("\t"); | ||
|
|
||
| // This only happens the first time, when we start reading the file | ||
| if (chromosome == null) { | ||
| logger.info("Parsing chr {} ", fields[0]); | ||
| currentChromosome = fields[0]; | ||
| chromosome = fields[0].split("\\.")[0]; | ||
| } | ||
|
|
||
| position = Integer.parseInt(fields[1]); | ||
| id = fields[2]; | ||
| ref = fields[3]; | ||
| alt = fields[4].split(","); | ||
| info = fields[7]; | ||
|
|
||
| String[] infoFields = info.split(";"); | ||
| flags = new ArrayList<>(); | ||
| SnpAnnotation snpAnnotation = new SnpAnnotation(); | ||
| for (String infoField : infoFields) { | ||
| String[] infoKeyValue = infoField.split("="); | ||
| switch (infoKeyValue[0]) { | ||
| case "GENEINFO": { | ||
| snpAnnotation.setGene(infoKeyValue[1].split(":")[0]); | ||
| break; | ||
| } | ||
| case "FREQ": { | ||
| String[] studies = infoKeyValue[1].split("\\|"); | ||
| List<PopulationFrequency> populationFrequencies = new ArrayList<>(); | ||
| for (String study : studies) { | ||
| String[] freqFields = study.split("[:,]"); | ||
| if (freqFields.length == alt.length + 2) { | ||
| for (int i = 0; i < alt.length; i++) { | ||
| if (".".equals(freqFields[i + 2])) { | ||
| logger.warn("Skipping pop. frequency for alt. allele ({}) of study {}: it is '.')", | ||
| alt[i], freqFields[0]); | ||
| } else { | ||
| PopulationFrequency populationFrequency = new PopulationFrequency(); | ||
| // Set study | ||
| populationFrequency.setStudy(freqFields[0]); | ||
| // Set reference | ||
| populationFrequency.setRefAllele(ref); | ||
| populationFrequency.setRefAlleleFreq(Float.parseFloat(freqFields[1])); | ||
| // Set alternate | ||
| populationFrequency.setAltAllele(alt[i]); | ||
| populationFrequency.setAltAlleleFreq(Float.parseFloat(freqFields[i + 2])); | ||
|
|
||
| populationFrequencies.add(populationFrequency); | ||
| } | ||
| } | ||
| } else { | ||
| logger.warn("Skipping pop. frequencies for study {}: the number of prop. frequencies ({}) does not" | ||
| + " match the number of alleles ({})", freqFields[0], freqFields.length - 1, | ||
| alt.length + 1); | ||
| } | ||
| } | ||
| snpAnnotation.setPopulationFrequencies(populationFrequencies); | ||
| break; | ||
| } | ||
| default: { | ||
| if (infoKeyValue.length == 1) { | ||
| flags.add(infoKeyValue[0]); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| snpAnnotation.setFlags(flags); | ||
|
|
||
| if (!currentChromosome.equals(fields[0])) { | ||
| logger.info("Parsing chr {} ", fields[0]); | ||
| } | ||
|
|
||
| Snp snp = new Snp(id, chromosome, position, ref, Arrays.asList(alt), "SNV", DBSNP_NAME, dbSnpUrlProperties.getVersion(), | ||
| snpAnnotation); | ||
| fileSerializer.serialize(snp, DBSNP_NAME); | ||
| } | ||
| } | ||
| } | ||
| logger.info("Parsing finished."); | ||
| } | ||
| } |
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