Examples with ArgsEngine cz1.util.ArgsEngine used on opensource projects

Example 6 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class Anchor1 method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-s", "--subject", true);
        myArgsEngine.add("-q", "--query", true);
        myArgsEngine.add("-b", "--blast", true);
        myArgsEngine.add("-k", "--kmer-size", true);
        myArgsEngine.add("-i", "--min-identity", true);
        myArgsEngine.add("-f", "--min-fraction", true);
        myArgsEngine.add("-di", "--diff-identity", true);
        myArgsEngine.add("-df", "--diff-fraction", true);
        myArgsEngine.add("-o", "--out-prefix", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-s")) {
        this.subject_file = myArgsEngine.getString("-s");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the subject/reference file.");
    }
    if (myArgsEngine.getBoolean("-q")) {
        this.query_file = myArgsEngine.getString("-q");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the query file.");
    }
    if (myArgsEngine.getBoolean("-k")) {
        this.kmer_size = Integer.parseInt(myArgsEngine.getString("-k"));
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the kmer size of contig construction.");
    }
    if (myArgsEngine.getBoolean("-b")) {
        this.blast_out = myArgsEngine.getString("-b");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the BLAST file.");
    }
    if (myArgsEngine.getBoolean("-o")) {
        this.out_prefix = myArgsEngine.getString("-o");
        if (new File(out_prefix + ".fa").exists() || new File(out_prefix + ".map").exists() || new File(out_prefix + "_unplaced.map").exists()) {
            throw new RuntimeException("Output files exist. Please specify a different name.");
        }
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the prefix of output files.");
    }
    if (myArgsEngine.getBoolean("-i")) {
        this.min_ident = 100 * Math.min(1.0, Double.parseDouble(myArgsEngine.getString("-i")));
    }
    if (myArgsEngine.getBoolean("-f")) {
        this.min_frac = Double.parseDouble(myArgsEngine.getString("-f"));
    }
    if (myArgsEngine.getBoolean("-di")) {
        this.diff_ident = Double.parseDouble(myArgsEngine.getString("-di"));
    }
    if (myArgsEngine.getBoolean("-df")) {
        this.diff_frac = Double.parseDouble(myArgsEngine.getString("-df"));
    }
}

Example 7 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class Consensus method setParameters.

@Override
public void setParameters(String[] args) {
    // TODO Auto-generated method stub
    if (myArgsEngine == null) {
        myArgsEngine = new ArgsEngine();
        myArgsEngine.add("-s", "--sequence", true);
        myArgsEngine.add("-m", "--map", true);
        myArgsEngine.add("-as", "--block-size", true);
        myArgsEngine.add("-bs", "--batch-size", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-l", "--min-size", true);
        myArgsEngine.add("-o", "--out", true);
        myArgsEngine.addWildOptions(bam_lib, true);
        myArgsEngine.addWildOptions(ins_lib, true);
        myArgsEngine.addWildOptions(w_lib, true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-s")) {
        this.sequence_file = myArgsEngine.getString("-s");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the contig file.");
    }
    if (myArgsEngine.getBoolean("-m")) {
        this.map_file = myArgsEngine.getString("-m");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the map file.");
    }
    if (myArgsEngine.getBoolean("-as")) {
        this.min_as = Integer.parseInt(myArgsEngine.getString("-as"));
    }
    if (myArgsEngine.getBoolean("-bs")) {
        this.batch_size = Integer.parseInt(myArgsEngine.getString("-bs"));
    }
    if (myArgsEngine.getBoolean("-t")) {
        this.THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-l")) {
        this.min_size = Integer.parseInt(myArgsEngine.getString("-l"));
    }
    if (myArgsEngine.getBoolean("-o")) {
        this.out_prefix = myArgsEngine.getString("-o");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the output file.");
    }
    this.parseDataLibrary(args);
}

Example 8 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class SamFileSplit 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-dir", true);
        myArgsEngine.add("-b", "--bed-dir", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        bam_in = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your BAM files.");
    }
    if (myArgsEngine.getBoolean("-b")) {
        bed_in = myArgsEngine.getString("-b");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your BED files.");
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-o")) {
        bam_out = myArgsEngine.getString("-o");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your output BAM files.");
    }
}

Example 9 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class SamToTaxa 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", "--index-file", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.add("-s", "--sam-file", true);
        myArgsEngine.add("-S", "--sorted", false);
        myArgsEngine.add("-x", "--max-coverage", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-s")) {
        mySamFileName = myArgsEngine.getString("-s");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the name of your SAM/BAM file.");
    }
    if (myArgsEngine.getBoolean("-i")) {
        myIndexFileName = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the index your FASTQ file.");
    }
    if (myArgsEngine.getBoolean("-S")) {
        mySamIsSorted = true;
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-o")) {
        myOutputDir = myArgsEngine.getString("-o");
    }
    if (myArgsEngine.getBoolean("-x")) {
        maxCov = Long.parseLong(myArgsEngine.getString("-x"));
    }
    this.makeOutputDir();
}

Example 10 with ArgsEngine

use of cz1.util.ArgsEngine in project polyGembler by c-zhou.

the class TagSequenceToFastq 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-tag", true);
        myArgsEngine.add("-t", "--threads", true);
        myArgsEngine.add("-o", "--prefix", true);
        myArgsEngine.parse(args);
    }
    if (myArgsEngine.getBoolean("-i")) {
        myInputDir = myArgsEngine.getString("-i");
    } else {
        printUsage();
        throw new IllegalArgumentException("Please specify the location of your FASTQ files.");
    }
    if (myArgsEngine.getBoolean("-t")) {
        THREADS = Integer.parseInt(myArgsEngine.getString("-t"));
    }
    if (myArgsEngine.getBoolean("-o")) {
        myOutputDir = myArgsEngine.getString("-o");
    }
    Utils.makeOutputDir(this.myOutputDir);
}