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

Example 6 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project org.hl7.fhir.core by hapifhir.

the class ClientHeadersTest method removeHeader.

@Test
@DisplayName("Happy path remove existing header.")
void removeHeader() {
    clientHeaders.addHeader(h1);
    clientHeaders.addHeader(h2);
    clientHeaders.addHeader(h3);
    clientHeaders.removeHeader(h2);
    Assertions.assertEquals(2, clientHeaders.headers().size());
    clientHeaders.removeHeader(new Header("header3", "value3"));
    Assertions.assertEquals(1, clientHeaders.headers().size());
}

Example 7 with Header

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

the class Gfa1ToGfa2 method call.

@Override
public Integer call() throws Exception {
    PrintWriter writer = null;
    try {
        writer = writer(outputGfa2File);
        final PrintWriter w = writer;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean header(final Header header) {
                // convert VN:Z:1.0 to VN:Z:2.0 annotation if present
                if (header.getAnnotations().containsKey("VN")) {
                    if (!"1.0".equals(header.getAnnotations().get("VN").getValue())) {
                        throw new RuntimeException("cannot convert input as GFA 1.0, was " + header.getAnnotations().get("VN").getValue());
                    }
                    Map<String, Annotation> annotations = new HashMap<String, Annotation>();
                    annotations.put("VN", new Annotation("VN", "Z", "2.0"));
                    for (Annotation annotation : header.getAnnotations().values()) {
                        if (!"VN".equals(annotation.getName())) {
                            annotations.put(annotation.getName(), annotation);
                        }
                    }
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(annotations), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Header(header.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean segment(final Segment segment) {
                if (segment.getSequence() != null) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), segment.getSequence().length(), segment.getSequence(), segment.getAnnotations()), w);
                } else if (segment.getAnnotations().containsKey("LN")) {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), Integer.parseInt(segment.getAnnotations().get("LN").getValue()), segment.getSequence(), segment.getAnnotations()), w);
                } else {
                    Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Segment(segment.getId(), 0, segment.getSequence(), segment.getAnnotations()), w);
                }
                return true;
            }

            @Override
            public boolean link(final Link link) {
                Position unknown = new Position(0, false);
                Alignment alignment = link.getOverlap() == null ? null : Alignment.valueOf(link.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(link.getSource()), toGfa2Reference(link.getTarget()), unknown, unknown, unknown, unknown, alignment, link.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean containment(final Containment containment) {
                Position unknown = new Position(0, false);
                Position targetStart = new Position(containment.getPosition(), false);
                Alignment alignment = containment.getOverlap() == null ? null : Alignment.valueOf(containment.getOverlap());
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Edge(null, toGfa2Reference(containment.getContainer()), toGfa2Reference(containment.getContained()), unknown, unknown, targetStart, unknown, alignment, containment.getAnnotations()), w);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                Gfa2Writer.write(new org.dishevelled.bio.assembly.gfa2.Path(path.getName(), toGfa2References(path.getSegments()), path.getAnnotations()), w);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            writer.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 8 with Header

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

the class SegmentsToCytoscapeNodes 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("\t");
                sb.append(segment.getSequenceOpt().orElse(""));
                sb.append("\t");
                sb.append(segment.containsLength() ? segment.getLength() : "");
                sb.append("\t");
                sb.append(segment.containsReadCount() ? segment.getReadCount() : "");
                sb.append("\t");
                sb.append(segment.containsFragmentCount() ? segment.getFragmentCount() : "");
                sb.append("\t");
                sb.append(segment.containsKmerCount() ? segment.getKmerCount() : "");
                sb.append("\t");
                sb.append(segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : "");
                sb.append("\t");
                sb.append(segment.getSequenceUriOpt().orElse(""));
                nw.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            nodesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 9 with Header

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

the class TraversalsToPropertyGraph 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) {
                if (!traversal.containsId()) {
                    throw new IllegalArgumentException("traversal identifiers are required for property graph CSV format");
                }
                StringBuilder sb = new StringBuilder();
                sb.append(traversal.getId());
                sb.append(",");
                sb.append(traversal.getSource().getName());
                sb.append(",");
                sb.append(traversal.getTarget().getName());
                sb.append(",");
                sb.append(traversal.getSource().getOrientation().getSymbol());
                sb.append(",");
                sb.append(traversal.getTarget().getOrientation().getSymbol());
                sb.append(",t,");
                sb.append(traversal.getPathName());
                sb.append(",");
                sb.append(traversal.getOrdinal());
                sb.append(",");
                sb.append(traversal.getOverlapOpt().orElse(""));
                ew.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            edgesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 10 with Header

use of org.dishevelled.bio.assembly.gfa1.Header in project okhttp by square.

the class Case method getHeaders.

public List<Header> getHeaders() {
    List<Header> result = new ArrayList<>();
    for (Map<String, String> inputHeader : headers) {
        Map.Entry<String, String> entry = inputHeader.entrySet().iterator().next();
        result.add(new Header(entry.getKey(), entry.getValue()));
    }
    return result;
}