Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

92
93
94
95
96
97
98
99
100
        Iterator<Feature> matchIter = MotifFinderSource.searchSingleStrand(motif, strand, null, posStart, shortSeq.getBytes());
        assertTrue("No matches found for motif " + motif, matchIter.hasNext());

        while(matchIter.hasNext()){
            Feature feat = matchIter.next();
            checkPatternMatches(motif, feat, shortSeq.getBytes());
        }
    }
View Full Code Here
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
        String motif = "TCTG";
        Strand strand = Strand.POSITIVE;

        Iterator<Feature> matchIter = MotifFinderSource.searchSingleStrand(motif, strand, null, posStart, shortSeq.getBytes());
        assertTrue("No matches found for motif " + motif, matchIter.hasNext());
        Feature feat = matchIter.next();

        assertEquals(posStart + 3, feat.getStart());
        assertEquals(posStart + 7, feat.getEnd());
        checkPatternMatches(motif, feat, shortSeq.getBytes());

        feat = matchIter.next();
        assertEquals(posStart + 14, feat.getStart());
        assertEquals(posStart + 18, feat.getEnd());
        checkPatternMatches(motif, feat, shortSeq.getBytes());


        assertFalse(matchIter.hasNext());
    }
View Full Code Here
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
        Iterator<Feature> iter = source.getFeatures(chr, start, end);

        if(expFeatStart >= 0){

            Feature feat = iter.next();
            assertNotNull(feat);

            assertEquals(expFeatStart, feat.getStart());

            if(expFeatureEnd > 0){
                assertEquals(expFeatureEnd, feat.getEnd());
            }

            checkPatternMatches(pattern, feat);
        }else{
            assertFalse("Iterator should be empty but isn't", iter.hasNext());
View Full Code Here
132
133
134
135
136
137
138
139
140
141
142
143
144
145
        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec);
        Iterator<Feature> iter = bfr.query("chr1", 0, Integer.MAX_VALUE);
        int count = 0;
        while (iter.hasNext()) {
            Feature feat = iter.next();
            if (count == 0) {
                //Check we don't skip first line
                assertEquals(1677535, feat.getStart() - startOffset);
            }
            count++;
        }
        assertEquals(6, count);
    }
View Full Code Here
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, codec);
        Iterator<Feature> iter = bfr.query(chr, start, end);
        int count = 0;
        while (iter.hasNext()) {
            Feature feat = iter.next();
            if (count == 0) {
                //Check we don't skip first line
                assertEquals(178707289, feat.getStart() - startOffset);
            }
            check_feat_unigene(feat, chr, start, end);
            count++;
        }

        assertEquals(71, count);

        //Re-query with some restrictions
        count = 0;
        start = 178709699;
        end = 179721089;
        iter = bfr.query(chr, start, end);
        while (iter.hasNext()) {
            Feature feat = iter.next();
            check_feat_unigene(feat, chr, start, end);
            count++;
        }

        assertEquals(65, count);
View Full Code Here
84
85
86
87
88
89
90
91
92
93
94

        IGV.getInstance().goToLocus("EGFR");
        FeatureTrack posTrack = (FeatureTrack) PosNegFeatureTracks.get(0);
        FeatureTrack negTrack = (FeatureTrack) PosNegFeatureTracks.get(1);
        Feature expFeature = new Locus("chr7", 55054248, 55054301);

        ReferenceFrame frame = FrameManager.getDefaultFrame();
        List<Feature> posFeats = posTrack.getFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd());

        assertEquals(1, posFeats.size());
View Full Code Here
202
203
204
205
206
207
208
209
210
211
212
213
214
215
            if (expChr.equalsIgnoreCase(".")) {
                continue;
            }

            Feature actFeature = actFeatures.get(ind);
            assertEquals(expChr, actFeature.getChr());
            assertEquals(expStart, actFeature.getStart());
            assertEquals(expEnd, actFeature.getEnd());

            ind++;

        }
View Full Code Here
228
229
230
231
232
233
234
235
236
237
238
239
240
        Iterator<Feature> features = combinedFeatureSource.getFeatures("chr1", 0, (int) 1e6);
        int ind = 0;
        int[] expStarts = new int[]{100, 200, 300};
        int[] expEnds = new int[]{101, 201, 301};
        while (features.hasNext()) {
            Feature feat = features.next();
            assertEquals(expStarts[ind], feat.getStart());
            assertEquals(expEnds[ind], feat.getEnd());
            ind++;
        }

        assertEquals(3, ind);
View Full Code Here
216
217
218
219
220
221
222
223
224
225
    @Test
    public void testBEDLoadsAliases() throws Exception {
        tstLoadFi(TestUtils.DATA_DIR + "bed/canFam2_alias.bed", 1, false);
        String[] aliases = new String[]{"AAAA", "BBB", "CCC"};
        for (String alias : aliases) {
            Feature feat = FeatureDB.getFeature(alias);
            assertNotNull(feat);
        }

    }
View Full Code Here
53
54
55
56
57
58
59
60
61
62
63
        AbstractFeatureReader bfs = AbstractFeatureReader.getFeatureReader(outPath, CodecFactory.getCodec(outPath, genome), false);
        Iterator<Feature> iter = bfs.iterator();
        int count = 0;
        while(iter.hasNext()){
            Feature feat = iter.next();

            assertTrue(overlapPred.apply(feat));

            count += 1;
        }
View Full Code Here
TOP

Related Classes of htsjdk.tribble.Feature

  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cli_plugin.PluginSource
  • org.broad.igv.das.DASFeatureSource$DasReader
  • org.broad.igv.data.expression.GeneToLocusHelper
  • org.broad.igv.dev.db.SQLCodecSourceTest
  • org.broad.igv.dev.db.SQLInputStreamTest
  • org.broad.igv.dev.db.UCSC_SQL_Test
  • org.broad.igv.feature.AbstractCacher
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.