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

Example 11 with Annotation

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

the class PathTest method setUp.

@Before
public void setUp() {
    id = "id";
    references = ImmutableList.of(Reference.valueOf("source+"), Reference.valueOf("target+"));
    annotations = ImmutableMap.<String, Annotation>builder().put("aa", new Annotation("aa", "i", "42")).build();
}

Example 12 with Annotation

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

the class SamReaderTest method testRoundTrip.

@Test
public void testRoundTrip() throws Exception {
    Map<String, Annotation> annotations = ImmutableMap.<String, Annotation>builder().put("NM", Annotation.valueOf("NM:i:0")).put("MD", Annotation.valueOf("MD:Z:101")).put("AS", Annotation.valueOf("AS:i:101")).put("XS", Annotation.valueOf("XS:i:55")).put("RG", Annotation.valueOf("RG:Z:NA12878-1")).put("MQ", Annotation.valueOf("MQ:i:60")).put("ms", Annotation.valueOf("ms:i:3614")).put("mc", Annotation.valueOf("mc:i:60612")).put("MC", Annotation.valueOf("MC:Z:101M")).put("ZB", Annotation.valueOf("ZB:B:i,1,2")).put("ZT", Annotation.valueOf("ZT:B:f,3.4,4.5")).build();
    SamRecord expected = new SamRecord("ERR194147.765130386", 99, "chr20", 60250, 60, "101M", "=", 60512, 363, "ACTCCATCCCATTCCATTCCACTCCCTTCATTTCCATTCCAGTCCATTCCATTCCATTCCATTCCATTCCACTCCACTCCATTCCATTCCACTGCACTCCA", "CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIIJJJJJJJJJJJJJHIIJIJGIJJJJJJJJJJJJJIJJJJJJJJJJJGGHHHFF@", annotations);
    File tmp = File.createTempFile("samReaderTest", ".sam");
    tmp.deleteOnExit();
    try (PrintWriter writer = new PrintWriter(new FileWriter(tmp))) {
        SamWriter.writeRecord(expected, writer);
    }
    SamRecord observed = records(tmp).iterator().next();
    assertEquals(expected.getQname(), observed.getQname());
    assertEquals(expected.getFlag(), observed.getFlag());
    assertEquals(expected.getRname(), observed.getRname());
    assertEquals(expected.getPos(), observed.getPos());
    assertEquals(expected.getMapq(), observed.getMapq());
    assertEquals(expected.getCigar(), observed.getCigar());
    assertEquals(expected.getRnext(), observed.getRnext());
    assertEquals(expected.getPnext(), observed.getPnext());
    assertEquals(expected.getTlen(), observed.getTlen());
    assertEquals(expected.getSeq(), observed.getSeq());
    assertEquals(expected.getQual(), observed.getQual());
    assertEquals(expected.getAnnotations(), observed.getAnnotations());
    assertEquals("B", observed.getAnnotations().get("ZB").getType());
    assertEquals("i", observed.getAnnotations().get("ZB").getArrayType());
    assertEquals(Integer.valueOf(1), observed.getAnnotationIntegers("ZB").get(0));
    assertEquals(Integer.valueOf(2), observed.getAnnotationIntegers("ZB").get(1));
    assertEquals("B", observed.getAnnotations().get("ZT").getType());
    assertEquals("f", observed.getAnnotations().get("ZT").getArrayType());
    assertEquals(Float.valueOf(3.4f), observed.getAnnotationFloats("ZT").get(0));
    assertEquals(Float.valueOf(4.5f), observed.getAnnotationFloats("ZT").get(1));
}

Example 13 with Annotation

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

the class Header method valueOf.

/**
 * Parse a header GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a header GFA 1.0 record parsed from the specified value
 */
public static Header valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("H"), "header value must start with H");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 1; 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 Header(annotations.build());
}

Example 14 with Annotation

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

the class Path method valueOf.

/**
 * Parse a path GFA 1.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a path GFA 1.0 record parsed from the specified value
 */
public static Path valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("P"), "path value must start with P");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 4) {
        throw new IllegalArgumentException("path value must have at least four tokens, was " + tokens.size());
    }
    String name = tokens.get(1);
    List<Reference> segments = "*".equals(tokens.get(2)) ? EMPTY_SEGMENTS : Splitter.on(",").splitToList(tokens.get(2)).stream().map(Reference::valueOf).collect(Collectors.toList());
    List<String> overlaps = "*".equals(tokens.get(3)) ? null : ImmutableList.copyOf(Splitter.on(",").split(tokens.get(3)));
    ImmutableMap.Builder<String, Annotation> annotations = ImmutableMap.builder();
    for (int i = 4; i < tokens.size(); i++) {
        String token = tokens.get(i);
        if (!token.isEmpty()) {
            Annotation annotation = Annotation.valueOf(token);
            annotations.put(annotation.getName(), annotation);
        }
    }
    return new Path(name, segments, overlaps, annotations.build());
}

Example 15 with Annotation

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

the class Path method valueOf.

/**
 * Parse a path GFA 2.0 record from the specified value.
 *
 * @param value value, must not be null
 * @return a path GFA 2.0 record parsed from the specified value
 */
public static Path valueOf(final String value) {
    checkNotNull(value);
    checkArgument(value.startsWith("O"), "path value must start with O");
    List<String> tokens = Splitter.on("\t").splitToList(value);
    if (tokens.size() < 3) {
        throw new IllegalArgumentException("path value must have at least three tokens, was " + tokens.size());
    }
    String id = "*".equals(tokens.get(1)) ? null : tokens.get(1);
    List<Reference> references = Splitter.on(" ").splitToList(tokens.get(2)).stream().map(Reference::valueOf).collect(Collectors.toList());
    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 Path(id, references, annotations.build());
}