uk.ac.ebi.eva.pipeline.io.writers.VepInputFlatFileWriter.java Source code

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Here is the source code for uk.ac.ebi.eva.pipeline.io.writers.VepInputFlatFileWriter.java

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/*
 * Copyright 2016 EMBL - European Bioinformatics Institute
 *
 * 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 uk.ac.ebi.eva.pipeline.io.writers;

import org.springframework.batch.item.file.FlatFileItemWriter;
import org.springframework.batch.item.file.transform.BeanWrapperFieldExtractor;
import org.springframework.batch.item.file.transform.DelimitedLineAggregator;
import org.springframework.core.io.FileSystemResource;

import uk.ac.ebi.eva.pipeline.model.VariantWrapper;
import java.io.File;

/**
 * Flat file writer of the input file used by VEP
 *
 * The file is listing all the coordinates of variants and nucleotide changes like:
 *  20   60343   60343   G/A   +
 *  20   60419   60419   A/G   +
 *  20   60479   60479   C/T   +
 *  ...
 *
 *  further format description: {@see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#input}
 */

public class VepInputFlatFileWriter extends FlatFileItemWriter<VariantWrapper> {

    /**
     * @return must return a {@link FlatFileItemWriter} and not a {@link org.springframework.batch.item.ItemWriter}
     * {@see https://jira.spring.io/browse/BATCH-2097
     *
     * TODO: The variant list should be compressed
     */
    public VepInputFlatFileWriter(File file) {
        super();

        BeanWrapperFieldExtractor<VariantWrapper> fieldExtractor = new BeanWrapperFieldExtractor<>();
        fieldExtractor.setNames(new String[] { "chr", "start", "end", "refAlt", "strand" });

        DelimitedLineAggregator<VariantWrapper> delLineAgg = new DelimitedLineAggregator<>();
        delLineAgg.setDelimiter("\t");
        delLineAgg.setFieldExtractor(fieldExtractor);

        setResource(new FileSystemResource(file));
        setAppendAllowed(false);
        setShouldDeleteIfExists(true);
        setLineAggregator(delLineAgg);
    }

    public VepInputFlatFileWriter(String filePath) {
        this(new File(filePath));
    }

}