// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript feature
SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf1.setValue("Parent", "gene:" + geneId);
- sf1.setValue("transcript_id", "transcript1");
+ sf1.setValue("Parent", geneId);
+ sf1.setValue("id", "transcript1");
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
0f, null);
- sf2.setValue("Parent", "gene:" + geneId);
- sf2.setValue("transcript_id", "transcript2");
+ sf2.setValue("Parent", geneId);
+ sf2.setValue("id", "transcript2");
genomic.addSequenceFeature(sf2);
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
- sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
- sf3.setValue("transcript_id", "transcript3");
+ sf3.setValue("Parent", geneId.toLowerCase());
+ sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
0f, null);
- sf4.setValue("Parent", "gene:XYZ");
- sf4.setValue("transcript_id", "transcript4");
+ sf4.setValue("Parent", "XYZ");
+ sf4.setValue("id", "transcript4");
genomic.addSequenceFeature(sf4);
EnsemblGene testee = new EnsemblGene();
EnsemblGene testee = new EnsemblGene();
SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
- sf.setValue("Parent", "gene:XYZ");
+ sf.setValue("Parent", "ßXYZ");
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
seq.addSequenceFeature(sf1);
// gene with wrong ID not valid
- SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf2.setValue("ID", "gene:XYZ");
+ SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
+ sf2.setValue("id", "XYZ");
seq.addSequenceFeature(sf2);
// gene with right ID is valid
- SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf3.setValue("ID", "gene:" + accId);
+ SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
+ sf3.setValue("id", accId);
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
- sf4.setValue("ID", "gene:" + accId);
+ sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf5.setValue("ID", "gene:" + accId);
+ sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("ID", "gene:" + accId);
+ sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblGene()