Examples with Annotation org.dishevelled.bio.annotation.Annotation used on opensource projects

Example 1 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled by heuermh.

the class AssemblyModel method traversalsFor.

/**
 * Create and return a list of path traversals for the specified path.
 *
 * @param path path, must not be null
 * @return a list of path traversals for the specified path
 */
static List<Traversal> traversalsFor(final Path path) {
    checkNotNull(path);
    int size = path.getSegments().size();
    List<Traversal> traversals = new ArrayList<Traversal>(size);
    Reference source = null;
    Reference target = null;
    String overlap = null;
    Map<String, Annotation> emptyAnnotations = Collections.emptyMap();
    for (int i = 0; i < size; i++) {
        target = path.getSegments().get(i);
        if (i > 0) {
            overlap = (path.getOverlaps() != null && path.getOverlaps().size() > i) ? path.getOverlaps().get(i - 1) : null;
        }
        if (source != null) {
            Traversal traversal = new Traversal(path.getName(), i - 1, source, target, overlap, emptyAnnotations);
            traversals.add(traversal);
        }
        source = target;
    }
    return traversals;
}

Example 2 with Annotation

use of org.dishevelled.bio.annotation.Annotation 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 3 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class GafRecord method valueOf.

/**
 * Parse a GAF record from the specified value.
 *
 * @param value value, must not be null
 * @return a GAF record parsed from the specified value
 */
public static GafRecord valueOf(final String value) {
    checkNotNull(value);
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 12) {
        throw new IllegalArgumentException("GAF record value must have at least twelve tokens, was " + tokens.size());
    }
    String queryName = tokens.get(0);
    long queryLength = Long.parseLong(tokens.get(1));
    long queryStart = Long.parseLong(tokens.get(2));
    long queryEnd = Long.parseLong(tokens.get(3));
    char strand = tokens.get(4).charAt(0);
    String pathName = tokens.get(5);
    long pathLength = Long.parseLong(tokens.get(6));
    long pathStart = Long.parseLong(tokens.get(7));
    long pathEnd = Long.parseLong(tokens.get(8));
    long matches = Long.parseLong(tokens.get(9));
    long alignmentBlockLength = Long.parseLong(tokens.get(10));
    int mappingQuality = Integer.parseInt(tokens.get(11));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 12; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(tokens.get(i));
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new GafRecord(queryName, queryLength, queryStart, queryEnd, strand, pathName, pathLength, pathStart, pathEnd, matches, alignmentBlockLength, mappingQuality, annotations.build());
}

Example 4 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class GenerateGaf method main.

public static void main(final String[] args) throws Exception {
    PrintWriter writer = null;
    try {
        writer = writer(null);
        for (int i = 0; i < 10_000_000; i++) {
            String queryName = "query";
            long queryLength = 1_000_000L;
            long queryStart = 20_000L;
            long queryEnd = 40_000L;
            char strand = '+';
            String pathName = "path";
            long pathLength = 20_000L;
            long pathStart = 2_000L;
            long pathEnd = 18_000L;
            long matches = 16_000L;
            long alignmentBlockLength = 16_000L;
            int mappingQuality = 60;
            ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
            annotations.put("cs", Annotation.valueOf("cs:Z:16000M"));
            writer.println(new GafRecord(queryName, queryLength, queryStart, queryEnd, strand, pathName, pathLength, pathStart, pathEnd, matches, alignmentBlockLength, mappingQuality, annotations.build()).toString());
        }
    } finally {
        try {
            writer.close();
        } catch (Exception e) {
        // empty
        }
    }
}

Example 5 with Annotation

use of org.dishevelled.bio.annotation.Annotation in project dishevelled-bio by heuermh.

the class Set method valueOf.

/**
 * Parse a set GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a set GFA 2.0 record parsed from the specified value
 */
public static Set valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("U"), "set value must start with U");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 3) {
        throw new IllegalArgumentException("set value must have at least three tokens, was " + tokens.size());
    }
    String id = "*".equals(tokens.get(1)) ? null : tokens.get(1);
    java.util.Set<String> ids = ImmutableSet.copyOf(Splitter.on(" ").split(tokens.get(2)));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 3; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Set(id, ids, annotations.build());
}