Examples with Gfa1Adapter org.dishevelled.bio.assembly.gfa1.Gfa1Adapter used on opensource projects

Example 6 with Gfa1Adapter

use of org.dishevelled.bio.assembly.gfa1.Gfa1Adapter in project dishevelled-bio by heuermh.

the class SegmentsToPropertyGraph method call.

@Override
public Integer call() throws Exception {
    PrintWriter nodesWriter = null;
    try {
        nodesWriter = writer(outputNodesFile);
        nodesWriter.println(HEADER);
        final PrintWriter nw = nodesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean segment(final Segment segment) {
                StringBuilder sb = new StringBuilder();
                sb.append(segment.getName());
                sb.append(",");
                sb.append(segment.getSequenceOpt().orElse(""));
                sb.append(",");
                sb.append(segment.containsLength() ? segment.getLength() : "");
                sb.append(",");
                sb.append(segment.containsReadCount() ? segment.getReadCount() : "");
                sb.append(",");
                sb.append(segment.containsFragmentCount() ? segment.getFragmentCount() : "");
                sb.append(",");
                sb.append(segment.containsKmerCount() ? segment.getKmerCount() : "");
                sb.append(",");
                sb.append(segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : "");
                sb.append(",");
                sb.append(segment.getSequenceUriOpt().orElse(""));
                nw.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            nodesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 7 with Gfa1Adapter

use of org.dishevelled.bio.assembly.gfa1.Gfa1Adapter in project dishevelled-bio by heuermh.

the class LinksToCytoscapeEdges method call.

@Override
public Integer call() throws Exception {
    PrintWriter edgesWriter = null;
    try {
        edgesWriter = writer(outputEdgesFile);
        edgesWriter.println(HEADER);
        final PrintWriter ew = edgesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean link(final Link link) {
                StringBuilder sb = new StringBuilder();
                sb.append(link.getSource().getName());
                sb.append("\t");
                sb.append(link.getSource().getOrientation().getSymbol());
                sb.append("\t");
                sb.append(link.getTarget().getName());
                sb.append("\t");
                sb.append(link.getTarget().getOrientation().getSymbol());
                sb.append("\tL\t");
                sb.append(link.getIdOpt().orElse(""));
                sb.append("\t");
                sb.append(link.getOverlapOpt().orElse(""));
                sb.append("\t");
                sb.append(link.containsMappingQuality() ? link.getMappingQuality() : "");
                sb.append("\t");
                sb.append(link.containsMismatchCount() ? link.getMismatchCount() : "");
                sb.append("\t");
                ew.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            edgesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 8 with Gfa1Adapter

use of org.dishevelled.bio.assembly.gfa1.Gfa1Adapter in project dishevelled-bio by heuermh.

the class LinksToPropertyGraph method call.

@Override
public Integer call() throws Exception {
    PrintWriter edgesWriter = null;
    try {
        edgesWriter = writer(outputEdgesFile);
        edgesWriter.println(HEADER);
        final PrintWriter ew = edgesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean link(final Link link) {
                if (!link.containsId()) {
                    throw new IllegalArgumentException("link identifiers are required for property graph CSV format");
                }
                StringBuilder sb = new StringBuilder();
                sb.append(link.getId());
                sb.append(",");
                sb.append(link.getSource().getName());
                sb.append(",");
                sb.append(link.getTarget().getName());
                sb.append(",");
                sb.append(link.getSource().getOrientation().getSymbol());
                sb.append(",");
                sb.append(link.getTarget().getOrientation().getSymbol());
                sb.append(",L,");
                sb.append(link.getOverlapOpt().orElse(""));
                sb.append(",");
                sb.append(link.containsMappingQuality() ? link.getMappingQuality() : "");
                sb.append(",");
                sb.append(link.containsMismatchCount() ? link.getMismatchCount() : "");
                ew.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            edgesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 9 with Gfa1Adapter

use of org.dishevelled.bio.assembly.gfa1.Gfa1Adapter in project dishevelled-bio by heuermh.

the class TraversalsToCytoscapeEdges method call.

@Override
public Integer call() throws Exception {
    PrintWriter edgesWriter = null;
    try {
        edgesWriter = writer(outputEdgesFile);
        edgesWriter.println(HEADER);
        final PrintWriter ew = edgesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean traversal(final Traversal traversal) {
                StringBuilder sb = new StringBuilder();
                sb.append(traversal.getSource().getName());
                sb.append("\t");
                sb.append(traversal.getSource().getOrientation().getSymbol());
                sb.append("\t");
                sb.append(traversal.getTarget().getName());
                sb.append("\t");
                sb.append(traversal.getTarget().getOrientation().getSymbol());
                sb.append("\tt\t");
                sb.append(traversal.getIdOpt().orElse(""));
                sb.append("\t");
                sb.append(traversal.getPathName());
                sb.append("\t");
                sb.append(traversal.getOrdinal());
                sb.append("\t");
                sb.append(traversal.getOverlapOpt().orElse(""));
                ew.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            edgesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}