Examples with GeneFeatureWithOriginalName io.repseq.cli.CLIUtils.GeneFeatureWithOriginalName used on opensource projects

Example 1 with GeneFeatureWithOriginalName

use of io.repseq.cli.CLIUtils.GeneFeatureWithOriginalName in project repseqio by repseqio.

the class TsvAction method go.

@Override
public void go(ActionHelper helper) throws Exception {
    VDJCLibraryRegistry reg = VDJCLibraryRegistry.getDefault();
    if (!"default".equals(params.getInput()))
        reg.registerLibraries(params.getInput());
    else
        reg.loadAllLibraries("default");
    Pattern chainPattern = params.chain == null ? null : Pattern.compile(params.chain);
    Pattern namePattern = params.name == null ? null : Pattern.compile(params.name);
    Long taxonFilter = params.taxonId;
    if (taxonFilter == null && params.species != null)
        taxonFilter = reg.resolveSpecies(params.species);
    try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(params.getOutputStream(), StandardCharsets.UTF_8))) {
        writer.write("Gene\tChains\tFeature\tStart\tStop\tSource\tSequence\n");
        for (VDJCLibrary lib : reg.getLoadedLibraries()) {
            if (taxonFilter != null && taxonFilter != lib.getTaxonId())
                continue;
            for (VDJCGene gene : lib.getGenes()) {
                if (chainPattern != null) {
                    boolean y = false;
                    for (String s : gene.getChains()) if (y |= chainPattern.matcher(s).matches())
                        break;
                    if (!y)
                        continue;
                }
                if (namePattern != null && !namePattern.matcher(gene.getName()).matches())
                    continue;
                for (GeneFeatureWithOriginalName feature : params.features) {
                    GeneFeature geneFeature = feature.feature;
                    NucleotideSequence featureSequence = gene.getFeature(geneFeature);
                    if (featureSequence == null)
                        continue;
                    // Don't output start and end positions for composite gene features
                    Long start = geneFeature.isComposite() ? null : gene.getData().getAnchorPoints().get(geneFeature.getFirstPoint());
                    Long end = geneFeature.isComposite() ? null : gene.getData().getAnchorPoints().get(geneFeature.getLastPoint());
                    NucleotideSequence nSequence = gene.getFeature(geneFeature);
                    List<String> tokens = Arrays.asList(gene.getGeneName(), gene.getChains().toString(), feature.originalName, // (so essentially 1-based inclusive). Report both as 1-based.
                    (start == null ? "" : params.isOneBased() ? String.valueOf(start + 1) : String.valueOf(start)), (end == null ? "" : String.valueOf(end)), gene.getData().getBaseSequence().getOrigin().toString(), nSequence.toString());
                    String delim = "";
                    for (String t : tokens) {
                        writer.write(delim);
                        writer.write(t);
                        delim = "\t";
                    }
                    writer.write('\n');
                }
            }
        }
    }
}