Java tutorial
/* * 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.variantstore.input.exomiser6.tsv; import org.phenotips.variantstore.input.AbstractVariantIterator; import org.phenotips.variantstore.input.VariantHeader; import org.phenotips.variantstore.shared.GACallInfoFields; import org.phenotips.variantstore.shared.GAVariantInfoFields; import org.phenotips.variantstore.shared.VariantUtils; import java.io.FileReader; import java.io.IOException; import java.io.Reader; import java.nio.file.Path; import java.util.Arrays; import java.util.Collections; import java.util.Iterator; import java.util.NoSuchElementException; import org.apache.commons.csv.CSVFormat; import org.apache.commons.csv.CSVParser; import org.apache.commons.csv.CSVRecord; import org.ga4gh.GACall; import org.ga4gh.GAVariant; import org.slf4j.Logger; import org.slf4j.LoggerFactory; /** * Parse the `*.variants.tsv` files returned by [Exomiser](http://www.sanger.ac.uk/science/tools/exomiser). Expose each * line as a ga4gh GAVariant object. * * @version $Id: d02cb9b4c3074fa3d3d64bce703a8728fd58f238 $ */ public class Exomiser6TSVIterator extends AbstractVariantIterator { private static Exomiser6TSVColumn[] columns = Exomiser6TSVColumn.values(); private Logger logger = LoggerFactory.getLogger(Exomiser6TSVIterator.class); private CSVParser tsvParser; private Iterator<CSVRecord> tsvRecordIterator; /** * Create a new TSV iterator for files output by Exomiser. * * @param path the path to the file * @param variantHeader the header with file meta-information */ public Exomiser6TSVIterator(Path path, VariantHeader variantHeader) { super(path, variantHeader); Reader reader = null; try { reader = new FileReader(this.path.toString()); this.tsvParser = CSVFormat.TDF.parse(reader); } catch (IOException e) { logger.error(String.format("Error when opening file %s, this should NOT be happening", this.path), e); } this.tsvRecordIterator = tsvParser.iterator(); // skip first row >.> if (this.hasNext()) { tsvRecordIterator.next(); } } @Override public boolean hasNext() { return this.tsvRecordIterator.hasNext(); } @Override public GAVariant next() { if (!this.hasNext()) { throw new NoSuchElementException(); } GAVariant variant = new GAVariant(); GACall call = new GACall(); variant.setCalls(Collections.singletonList(call)); double exacFreq = 0; int i = 0; for (String field : tsvRecordIterator.next()) { // try to add the field different ways, see what sticks. addFieldToVariant(variant, field, i); addFieldToVariantInfo(variant, field, i); addGenotypeToVariant(call, field, i); addFieldToCallInfo(call, field, i); exacFreq = getMaxExacFreqFromField(exacFreq, field, i); i++; } if (exacFreq != 0) { VariantUtils.addInfo(variant, GAVariantInfoFields.EXAC_AF, String.valueOf(exacFreq)); } variant.setEnd(variant.getStart() + variant.getReferenceBases().length()); if (!this.hasNext()) { // Cleanup try { tsvParser.close(); } catch (IOException e) { logger.error(String.format("Error when closing file %s", this.path), e); } } return variant; } private void addFieldToVariant(GAVariant variant, String field, int i) { switch (columns[i]) { case CHROM: variant.setReferenceName(field); break; case POS: // GA4GH uses 0-based indexing, unlike VCF's 1-based. variant.setStart(Long.valueOf(field) - 1); break; case REF: variant.setReferenceBases(field); break; case ALT: variant.setAlternateBases(Arrays.asList(field.split(","))); break; default: } } private void addFieldToVariantInfo(GAVariant variant, String field, int i) { switch (columns[i]) { case EXOMISER_GENE: VariantUtils.addInfo(variant, GAVariantInfoFields.GENE, field); break; case FUNCTIONAL_CLASS: VariantUtils.addInfo(variant, GAVariantInfoFields.GENE_EFFECT, field); break; default: } } private void addGenotypeToVariant(GACall call, String field, int i) { switch (columns[i]) { case GENOTYPE: String splitter = "/"; String phasedSplitter = "|"; if (!field.contains(splitter)) { if (field.contains(phasedSplitter)) { // phased splitter = phasedSplitter; } else { //TODO: SHOULD NOT BE DOING THIS. call.setGenotype(Arrays.asList(0, 0)); break; } } String[] split = field.split(splitter); if (".".equals(split[0])) { //TODO: SHOULD NOT BE DOING THIS. call.setGenotype(Arrays.asList(0, 0)); break; } call.setGenotype(Arrays.asList(Integer.valueOf(split[0]), Integer.valueOf(split[1]))); break; default: } } private void addFieldToCallInfo(GACall call, String field, int i) { switch (columns[i]) { case QUAL: VariantUtils.addInfo(call, GACallInfoFields.QUALITY, field); break; case FILTER: VariantUtils.addInfo(call, GACallInfoFields.FILTER, field); break; case EXOMISER_VARIANT_SCORE: VariantUtils.addInfo(call, GACallInfoFields.EXOMISER_VARIANT_SCORE, field); break; case EXOMISER_GENE_PHENO_SCORE: VariantUtils.addInfo(call, GACallInfoFields.EXOMISER_GENE_PHENO_SCORE, field); break; case EXOMISER_GENE_COMBINED_SCORE: VariantUtils.addInfo(call, GACallInfoFields.EXOMISER_GENE_COMBINED_SCORE, field); break; case EXOMISER_GENE_VARIANT_SCORE: VariantUtils.addInfo(call, GACallInfoFields.EXOMISER_GENE_VARIANT_SCORE, field); break; default: } } private double getMaxExacFreqFromField(double exacFreq, String field, int i) { switch (columns[i]) { case MAX_FREQUENCY: if (!".".equals(field)) { return Math.max(exacFreq, Double.parseDouble(field)); } break; default: } return 0; } }