biospectra.verification.MetagenomicReadGenerator.java Source code

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Here is the source code for biospectra.verification.MetagenomicReadGenerator.java

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/*
 * Copyright 2015 iychoi.
 *
 * 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 biospectra.verification;

import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import java.util.List;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.yeastrc.fasta.FASTAEntry;

/**
 *
 * @author iychoi
 */
public class MetagenomicReadGenerator implements Closeable {
    private static final Log LOG = LogFactory.getLog(MetagenomicReadGenerator.class);

    private List<File> fastaDocs;
    private RandomReadSampler readSampler;
    private SequencingArtifactsSimulator artifactsSimulator;

    public MetagenomicReadGenerator(List<File> fastaDocs) throws Exception {
        if (fastaDocs == null) {
            throw new IllegalArgumentException("fastaDocs is null");
        }

        initialize(fastaDocs);
    }

    private void initialize(List<File> fastaDocs) throws Exception {
        this.fastaDocs = fastaDocs;
        this.readSampler = new RandomReadSampler(fastaDocs);
        this.artifactsSimulator = new SequencingArtifactsSimulator();
    }

    public FASTAEntry generate(int readSize, double errorRatio) throws Exception {
        if (readSize <= 0) {
            throw new IllegalArgumentException("readSize must be larger than 0");
        }

        if (errorRatio < 0 || errorRatio > 1) {
            throw new IllegalArgumentException("errorRatio must be a positive value between 0 and 1");
        }

        FASTAEntry sample = this.readSampler.sample(readSize);
        String newSequence = this.artifactsSimulator.noise(sample.getSequence(), errorRatio);

        return new FASTAEntry(sample.getHeaders(), newSequence, sample.getHeaderLine());
    }

    @Override
    public void close() throws IOException {
        this.fastaDocs.clear();
        this.readSampler.close();
    }
}