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

Example 6 with Barcode

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

the class ParseBarcodeRead method findBestBarcode.

/**
 * Returns the best barcode match for a given sequence.
 * @param queryS query sequence to be tested against all barcodes
 * @param maxDivergence maximum divergence to permit
 * @return best barcode match (null if no good match)
 */
Barcode findBestBarcode(String queryS, int maxDivergence) {
    long query = BaseEncoder.getLongFromSeq(queryS.substring(0, chunkSize));
    // note because the barcodes are polyA after the sequence, they should always
    // sort ahead of the hit, this is the reason for the -(closestHit+2)
    int closestHit = Arrays.binarySearch(quickBarcodeList, query);
    // Below is the old pipeline approach, which works (at least for maxDivergence of 0)
    if (closestHit < -1) {
        // should always be true, as the barcode+overhang is padded to 32 bases with polyA
        int index = quickMap.get(quickBarcodeList[-(closestHit + 2)]);
        if (theBarcodes[index].compareSequence(query, 1) == 0) {
            return theBarcodes[index];
        } else if (maxDivergence == 0) {
            // return null if not a perfect match
            return null;
        }
    } else {
        // should never go to this line
        return null;
    }
    int maxLength = 0, minDiv = maxDivergence + 1;
    Barcode bestBC = null;
    for (Barcode bc : theBarcodes) {
        int div = bc.compareSequence(query, maxDivergence + 1);
        if (div <= minDiv) {
            if ((div < minDiv) || (bc.getBarOverLength() > maxLength)) {
                minDiv = div;
                maxLength = bc.getBarOverLength();
                bestBC = bc;
            } else {
                // it is a tie, so return that not resolvable
                bestBC = null;
            }
        }
    }
    return bestBC;
}

Example 7 with Barcode

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

the class FastqToTagSequence method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-i", "--input-fastq", true);
        myArgsEngine.add("-k", "--key-file", true);
        myArgsEngine.add("-e", "--enzyme", true);
        myArgsEngine.add("-q", "--min-qualS", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-T", "--trim-leading", true);
        myArgsEngine.add("-b", "--unassgined-reads", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        myInputDirName = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your FASTQ files.");
    }
    if (myArgsEngine.getBoolean("-k")) {
        myKeyfile = myArgsEngine.getString("-k");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify a barcode key file.");
    }
    if (myArgsEngine.getBoolean("-e")) {
        myEnzyme = myArgsEngine.getString("-e").split("-");
    } else {
        myLogger.warn("No enzyme specified.  Using enzyme listed in key file.");
        try {
            BufferedReader br = Utils.getBufferedReader(myKeyfile);
            String[] s = br.readLine().split("\\s+");
            int k = -1;
            for (int i = 0; i < s.length; i++) if (s[i].toLowerCase().equals("enzyme"))
                k = i;
            if (k < 0)
                throw new IllegalArgumentException("No enzyme found in the key file. " + "Please specify the enzyme with -e option.\n\n");
            s = br.readLine().split("\\s+");
            myEnzyme = s[k].split("-");
            br.close();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    if (myArgsEngine.getBoolean("-q")) {
        myMinQualS = Integer.parseInt(myArgsEngine.getString("-q"));
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-T")) {
        int leading = Integer.parseInt(myArgsEngine.getString("-T"));
        if (leading > 0) {
            List<Integer> leadings = new ArrayList<Integer>();
            leadings.add(leading);
            for (int i = 1; i < 4; i++) {
                if (leading - i >= 0)
                    leadings.add(leading - i);
                leadings.add(leading + i);
            }
            myLeadingTrim = new int[leadings.size()];
            for (int i = 0; i < myLeadingTrim.length; i++) myLeadingTrim[i] = leadings.get(i);
        }
    }
    if (myArgsEngine.getBoolean("-o")) {
        myOutputDir = myArgsEngine.getString("-o");
    }
    this.makeOutputDir();
}

Example 8 with Barcode

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

the class SamFileExtract method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-i", "--input-file", true);
        myArgsEngine.add("-b", "--bed-dir", true);
        myArgsEngine.add("-o", "--output-file", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        bam_in = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your FASTQ files.");
    }
    if (myArgsEngine.getBoolean("-b")) {
        bed_in = myArgsEngine.getString("-b");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify a barcode key file.");
    }
    if (myArgsEngine.getBoolean("-o")) {
        bam_out = myArgsEngine.getString("-o");
    } else {
        myLogger.warn("No enzyme specified.  Using enzyme listed in key file.");
    }
}

Example 9 with Barcode

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

the class GBSSimulator method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (args.length == 0) {
        printUsage();
        throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
    }
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-f", "--fasta-file", true);
        myArgsEngine.add("-e", "--enzyme", true);
        myArgsEngine.add("-l", "--library", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-b", "--barcode-file", true);
        myArgsEngine.add("-m", "--avg-depth", true);
        myArgsEngine.add("-s", "--sdev", true);
        myArgsEngine.add("-S", "--random-seed", true);
        myArgsEngine.add("-q", "--quality-file", true);
        myArgsEngine.add("-o", "--output-file", true);
        myArgsEngine.parse(args);
    }
    String fastaFileDir, enzymeName = "PstI", libPrepFilePath = null, barcodeFilePath = null, params = null, outputDir = "./";
    double avg = 5, sd = 5;
    long RANDOM_SEED = System.nanoTime();
    if (myArgsEngine.getBoolean("-f")) {
        fastaFileDir = myArgsEngine.getString("-f");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the FASTA files.");
    }
    if (myArgsEngine.getBoolean("-e")) {
        enzymeName = myArgsEngine.getString("-e");
    }
    if (myArgsEngine.getBoolean("-l")) {
        libPrepFilePath = myArgsEngine.getString("-l");
    }
    if (myArgsEngine.getBoolean("-b")) {
        barcodeFilePath = myArgsEngine.getString("-b");
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-m")) {
        avg = Double.parseDouble(myArgsEngine.getString("-m"));
    }
    if (myArgsEngine.getBoolean("-s")) {
        sd = Double.parseDouble(myArgsEngine.getString("-s"));
    }
    if (myArgsEngine.getBoolean("-S")) {
        RANDOM_SEED = Long.parseLong(myArgsEngine.getString("-S"));
    }
    if (myArgsEngine.getBoolean("-q")) {
        params = myArgsEngine.getString("-q");
    }
    if (myArgsEngine.getBoolean("-o")) {
        outputDir = myArgsEngine.getString("-o");
    }
    gbs = new GBS(fastaFileDir, enzymeName, avg, sd, params, libPrepFilePath, barcodeFilePath, outputDir, RANDOM_SEED);
}