Examples with Chromosome PedigreeSim.Chromosome used on opensource projects

Example 1 with Chromosome

use of PedigreeSim.Chromosome in project polyGembler by c-zhou.

the class Population method writeGenomeFile.

public void writeGenomeFile(int sim_sample_index) {
    final int N = popData.chromCount();
    String[][] indall;
    // StringBuilder chr;
    ArrayList<Locus> loci;
    int pos;
    String str2write;
    Individual indiv = popData.getIndiv(sim_sample_index);
    try (BufferedWriter bw = getGZIPBufferedWriter(filePath + SEP + scenario + SEP + indiv.getIndivName() + ".fasta.gz")) {
        for (int c = 0; c < N; c++) {
            Chromosome chrom = popData.getChrom(c);
            Chromosome0 chr = chromosome[c];
            loci = chrom.getLocus();
            indall = new String[PLOIDY][loci.size()];
            for (int l = 0; l < loci.size(); l++) {
                String[] inds = indiv.getLocusAllele(c, l);
                for (int h = 0; h < PLOIDY; h++) {
                    indall[h][l] = inds[h];
                }
            }
            for (int h = 0; h < PLOIDY; h++) {
                // debug
                // println(getSystemTime()+" >>> StringBulder starting...");
                /**
                 * String builder is slow
                 *                        chr = new StringBuilder(ref.substring(cutsite[c],cutsite[c+1]));
                 *                        for(int l=0; l<loci.size(); l++) {
                 *                            pos = SNPs2PosMap.get(loci.get(l).getLocusName());
                 *                            chr.replace(pos,pos+indall[h][l].length(),indall[h][l]);
                 *                        }
                 */
                // debug
                // println(getSystemTime()+" >>> Done. BufferedWriter Start writing...");
                String header = ">" + chr.getName() + "|" + (h + 1) + ":" + PLOIDY;
                bw.write(header + NLS);
                final StringBuilder oos = new StringBuilder();
                int j0 = 0, j1 = chr.getLBasePairs();
                for (int l = 0; l < loci.size(); l++) {
                    pos = SNPs2PosMap.get(loci.get(l).getLocusName());
                    str2write = indall[h][l];
                    oos.append(chr.getDnaSEQ().substring(j0, pos - str2write.length() + 1));
                    oos.append(str2write);
                    j0 = pos + str2write.length();
                }
                if (j0 < j1)
                    oos.append(chr.getDnaSEQ().substring(j0, j1));
                bw.write(this.formatOutput(oos.toString()));
                // debug
                myLogger.info(getSystemTime() + " " + header + " >>> done.");
            }
        }
        bw.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }
}