Example usage for java.lang String String

Introduction

In this page you can find the example usage for java.lang String String.

Prototype

public String(byte bytes[], int offset, int length) 

Source Link

Document

Constructs a new String by decoding the specified subarray of bytes using the platform's default charset.

Usage

From source file:edu.msu.cme.rdp.readseq.utils.QualityTrimmer.java

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("f", "fastq-out", false, "Write fastq instead of fasta file");
    options.addOption("l", "less-than", false, "Trim at <= instead of strictly =");
    options.addOption("i", "illumina", false, "Illumina trimming mode");

    FastqWriter fastqOut = null;/*w  w  w . ja v a 2 s .  c  o m*/
    FastaWriter fastaOut = null;

    byte qualTrim = -1;

    boolean writeFasta = true;
    boolean trimle = false;
    boolean illumina = false;

    List<SeqReader> readers = new ArrayList();
    List<File> seqFiles = new ArrayList();

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("fastq-out")) {
            writeFasta = false;
        }

        if (line.hasOption("less-than")) {
            trimle = true;
        }
        if (line.hasOption("illumina")) {
            illumina = true;
        }

        args = line.getArgs();

        if (args.length < 2) {
            throw new Exception("Unexpected number of arguments");
        }

        if (args[0].length() != 1) {
            throw new Exception("Expected single character quality score");
        }

        qualTrim = FastqCore.Phred33QualFunction.translate(args[0].charAt(0));

        for (int index = 1; index < args.length; index++) {
            File seqFile = new File(args[index]);
            SeqReader reader;
            if (SeqUtils.guessFileFormat(seqFile) == SequenceFormat.FASTA) {
                if (index + 1 == args.length) {
                    throw new Exception("Fasta files must be immediately followed by their quality file");
                }

                File qualFile = new File(args[index + 1]);
                if (SeqUtils.guessFileFormat(qualFile) != SequenceFormat.FASTA) {
                    throw new Exception(seqFile + " was not followed by a fasta quality file");
                }

                reader = new QSeqReader(seqFile, qualFile);
                index++;
            } else {
                if (seqFile.getName().endsWith(".gz")) {
                    reader = new SequenceReader(new GZIPInputStream(new FileInputStream(seqFile)));
                } else {
                    reader = new SequenceReader(seqFile);
                }
            }

            readers.add(reader);
            seqFiles.add(seqFile);
        }
    } catch (Exception e) {
        new HelpFormatter().printHelp("USAGE: QualityTrimmer [options] <ascii_score> <seq_file> [qual_file]",
                options, true);
        System.err.println("Error: " + e.getMessage());
        System.exit(1);
    }

    for (int readerIndex = 0; readerIndex < readers.size(); readerIndex++) {
        File seqFile = seqFiles.get(readerIndex);
        String outStem = "trimmed_" + seqFile.getName().substring(0, seqFile.getName().lastIndexOf("."));
        if (writeFasta) {
            fastaOut = new FastaWriter(outStem + ".fasta");
        } else {
            fastqOut = new FastqWriter(outStem + ".fastq", FastqCore.Phred33QualFunction);
        }

        int[] lengthHisto = new int[200];

        SeqReader reader = readers.get(readerIndex);

        QSequence qseq;

        long totalLength = 0;
        int totalSeqs = 0;
        long trimmedLength = 0;
        int trimmedSeqs = 0;

        int zeroLengthAfterTrimming = 0;

        long startTime = System.currentTimeMillis();

        while ((qseq = (QSequence) reader.readNextSequence()) != null) {
            char[] bases = qseq.getSeqString().toCharArray();
            byte[] qual = qseq.getQuality();

            if (bases.length != qual.length) {
                System.err.println(qseq.getSeqName() + ": Quality length doesn't match seq length for seq");
                continue;
            }

            totalSeqs++;
            totalLength += bases.length;

            int trimIndex = -1;
            if (illumina && qual[bases.length - 1] == qualTrim) {
                trimIndex = bases.length - 1;
                while (trimIndex >= 0 && qual[trimIndex] == qualTrim) {
                    trimIndex--;
                }

                trimIndex++; //Technically we're positioned over the first good base, move back to the last bad base
            } else if (!illumina) {
                for (int index = 0; index < bases.length; index++) {
                    if (qual[index] == qualTrim || (trimle && qual[index] < qualTrim)) {
                        trimIndex = index;
                        break;
                    }
                }
            }

            String outSeq;
            byte[] outQual;
            if (trimIndex == -1) {
                outSeq = qseq.getSeqString();
                outQual = qseq.getQuality();
            } else {
                outSeq = new String(bases, 0, trimIndex);
                outQual = Arrays.copyOfRange(qual, 0, trimIndex);
                trimmedSeqs++;
            }
            int len = outSeq.length();
            trimmedLength += len;

            if (len >= lengthHisto.length) {
                lengthHisto = Arrays.copyOf(lengthHisto, len + 1);
            }
            lengthHisto[len]++;

            if (outSeq.length() == 0) {
                //System.err.println(qseq.getSeqName() + ": length 0 after trimming");
                zeroLengthAfterTrimming++;
                continue;
            }

            if (writeFasta) {
                fastaOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq);
            } else {
                fastqOut.writeSeq(qseq.getSeqName(), qseq.getDesc(), outSeq, outQual);
            }
        }

        reader.close();

        if (writeFasta) {
            fastaOut.close();
        } else {
            fastqOut.close();
        }

        System.out.println(
                "Processed " + seqFile + " in " + (System.currentTimeMillis() - startTime) / 1000.0 + "s");
        System.out.println("Before trimming:");
        System.out.println("Total Sequences:           " + totalSeqs);
        System.out.println("Total Sequence Data:       " + totalLength);
        System.out.println("Average sequence length:   " + ((float) totalLength / totalSeqs));
        System.out.println();
        System.out.println("After trimming:");
        System.out.println("Total Sequences:           " + (totalSeqs - zeroLengthAfterTrimming));
        System.out.println("Sequences Trimmed:         " + trimmedSeqs);
        System.out.println("Total Sequence Data:       " + trimmedLength);
        System.out.println("Average sequence length:   "
                + ((float) trimmedLength / (totalSeqs - zeroLengthAfterTrimming)));
        System.out.println();

        System.out.println("Length\tCount");
        for (int index = 0; index < lengthHisto.length; index++) {
            if (lengthHisto[index] == 0) {
                continue;
            }

            System.out.println(index + "\t" + lengthHisto[index]);
        }

        System.out.println();
        System.out.println();
        System.out.println();
    }
}

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From source file:Main.java

public static String str(char[] ch, int start, int length) {
    return new String(ch, start, length);
}

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From source file:Main.java

public static String bytes2String(byte[] b, int start, int len) {
    return new String(b, start, len);
}

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