Examples with Digest cz1.gbs.core.Digest used on opensource projects

Example 1 with Digest

use of cz1.gbs.core.Digest in project polyGembler by c-zhou.

the class GBS method simulate.

public void simulate(final int sim_sample_index) {
    try {
        // GBSFastqFileBufferedWriter = getGZIPBufferedWriter(GBSFastqFilePath);
        String name, line, fastaFilePath;
        ArrayList<Integer> cut, recognization;
        StringBuilder chromosome;
        FastqRead fastq;
        int l;
        Digest digestion;
        fastaFilePath = fastaFileList.get(sim_sample_index);
        StringBuilder oos = new StringBuilder();
        // try{
        BufferedWriter GBSFastqFileBufferedWriter = getGZIPBufferedWriter(GBSFastqFilePath + "_" + sim_sample_index + ".gz", 65536);
        BufferedReader br = getBufferedReader(fastaFilePath);
        line = br.readLine();
        while (line != null) {
            name = parseSampleName(fastaFilePath) + "|" + line.replaceFirst(">", "");
            chromosome = new StringBuilder();
            while ((line = br.readLine()) != null && !line.startsWith(">")) {
                chromosome.append(line);
            }
            l = chromosome.length();
            // System.out.println(getSystemTime()+">>> digest starting...");
            digestion = new Digest(enzyme, chromosome.toString());
            // System.out.println(getSystemTime()+">>> done.");
            cut = digestion.getCutsite();
            recognization = digestion.getRecognization();
            // System.out.println(getSystemTime()+">>> simulate starting...");
            // simulate 5'-3' end genome
            int coverage;
            for (int i = 2; i < cut.size(); i++) {
                if (cut.get(i) - cut.get(i - 1) < MIN_FRAGMENT_SIZE)
                    continue;
                coverage = (int) Math.round(meanDepth + random.nextGaussian() * sdDepth);
                for (int j = 0; j < coverage; j++) {
                    fastq = generateFastqRead(chromosome.substring(cut.get(i - 1), cut.get(i)), recognization.get(i - 1), fastaFileBarcodeMap.get(fastaFilePath), "@" + name + "|" + cut.get(i - 1) + "|" + j, false);
                    // writeFastqRead(fastq);
                    oos.setLength(0);
                    oos.append(fastq.identifier);
                    oos.append(NLS);
                    oos.append(fastq.sequence);
                    oos.append(NLS);
                    oos.append(fastq.plus);
                    oos.append(NLS);
                    oos.append(fastq.quality);
                    oos.append(NLS);
                    GBSFastqFileBufferedWriter.write(oos.toString());
                }
            }
            // simulate reverse complementary genome
            chromosome.reverse();
            for (int i = 0; i < l; i++) chromosome.setCharAt(i, baseComplementaryMap.get(chromosome.charAt(i)));
            for (int i = 0; i < cut.size(); i++) cut.set(i, l - cut.get(i));
            Collections.reverse(cut);
            for (int i = 2; i < cut.size(); i++) {
                if (cut.get(i) - cut.get(i - 1) < MIN_FRAGMENT_SIZE)
                    continue;
                coverage = (int) Math.round(meanDepth + random.nextGaussian() * sdDepth);
                for (int j = 0; j < coverage; j++) {
                    fastq = generateFastqRead(chromosome.substring(cut.get(i - 1), cut.get(i)), recognization.get(i - 1), fastaFileBarcodeMap.get(fastaFilePath), "@" + name + "|" + cut.get(i - 1) + "|1", true);
                    // writeFastqRead(fastq);
                    oos.setLength(0);
                    oos.append(fastq.identifier);
                    oos.append(NLS);
                    oos.append(fastq.sequence);
                    oos.append(NLS);
                    oos.append(fastq.plus);
                    oos.append(NLS);
                    oos.append(fastq.quality);
                    oos.append(NLS);
                    GBSFastqFileBufferedWriter.write(oos.toString());
                }
            }
            // System.out.println(getSystemTime()+">>> done.");
            System.out.println(getSystemTime() + ">>> " + name + " done.");
        }
        br.close();
        GBSFastqFileBufferedWriter.close();
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
    }
// GBSFastqFileBufferedWriter.close();
// } catch (IOException | InterruptedException e) {
// } catch (InterruptedException e) {
// e.printStackTrace();
// System.exit(1);
// }
}