biospectra.verification.RandomReadSampler.java Source code

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Here is the source code for biospectra.verification.RandomReadSampler.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 biospectra.utils.FastaFileReader;
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.yeastrc.fasta.FASTAEntry;
import org.yeastrc.fasta.FASTAReader;

/**
 *
 * @author iychoi
 */
public class RandomReadSampler implements Closeable {

    private static final Log LOG = LogFactory.getLog(RandomReadSampler.class);

    private List<File> fastaDocs;
    private List<ReadInfo> readInfo;
    private long rangeMax;
    private Random random;

    public RandomReadSampler(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;

        // precompute readinfo
        this.readInfo = makeReadInfo(fastaDocs);
        this.rangeMax = 0;
        for (ReadInfo ri : this.readInfo) {
            this.rangeMax += ri.getSize();
        }

        this.random = new Random();
    }

    private List<ReadInfo> makeReadInfo(List<File> fastaDocs) throws Exception {
        List<ReadInfo> readInfoArr = new ArrayList<ReadInfo>();
        for (File fastaDoc : fastaDocs) {
            readInfoArr.addAll(makeReadInfo(fastaDoc));
        }
        return readInfoArr;
    }

    private List<ReadInfo> makeReadInfo(File fastaDoc) throws Exception {
        List<ReadInfo> readInfoArr = new ArrayList<ReadInfo>();
        FASTAReader reader = FastaFileReader.getFASTAReader(fastaDoc);
        FASTAEntry read = null;

        int id = 0;
        while ((read = reader.readNext()) != null) {
            String sequence = read.getSequence();
            ReadInfo info = new ReadInfo(fastaDoc, id, sequence.length());
            readInfoArr.add(info);
            id++;
        }

        reader.close();
        return readInfoArr;
    }

    private boolean isATGCSequence(String seq) {
        for (int i = 0; i < seq.length(); i++) {
            char s = seq.charAt(i);
            if (s != 'A' && s != 'T' && s != 'G' && s != 'C') {
                return false;
            }
        }
        return true;
    }

    private FASTAEntry trySample(int readSize) throws Exception {
        long random = Math.abs(this.random.nextLong()) % this.rangeMax;
        long left = random;
        for (ReadInfo ri : this.readInfo) {
            if (left <= ri.getSize()) {
                if (ri.getSize() - left >= readSize) {
                    // go for it
                    FASTAReader reader = FastaFileReader.getFASTAReader(ri.getFastaFile());
                    FASTAEntry read = null;
                    int id = 0;
                    while ((read = reader.readNext()) != null) {
                        if (id == ri.getId()) {
                            String sequence = read.getSequence().substring((int) left, (int) (left + readSize));
                            if (isATGCSequence(sequence)) {
                                FASTAEntry entry = new FASTAEntry(read.getHeaders(), sequence,
                                        read.getHeaderLine());
                                return entry;
                            } else {
                                return null;
                            }
                        }
                        id++;
                    }
                    return null;
                } else {
                    return null;
                }
            } else {
                left -= ri.getSize();

                if (left <= 0) {
                    break;
                }
            }
        }
        return null;
    }

    public FASTAEntry sample(int readSize) throws Exception {
        FASTAEntry entry = null;
        int variant = this.random.nextInt(readSize / 5) - (readSize / 10);
        int newReadSize = readSize + variant;
        if (newReadSize <= 0) {
            newReadSize = readSize;
        }

        do {
            entry = trySample(newReadSize);
        } while (entry == null);

        return entry;
    }

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