// CDS at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS belonging to a different transcript doesn't count
sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// exon feature doesn't count
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+ sf = new SequenceFeature("anotherType", "", 20000,
20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
// cds with wrong parent not valid
SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf2.setValue("Parent", "transcript:XYZ");
+ sf2.setValue("Parent", "XYZ");
seq.addSequenceFeature(sf2);
// cds with right parent is valid
SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf3.setValue("Parent", "transcript:" + accId);
+ sf3.setValue("Parent", accId);
seq.addSequenceFeature(sf3);
// cds sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
null);
- sf4.setValue("Parent", "transcript:" + accId);
+ sf4.setValue("Parent", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf5.setValue("Parent", "transcript:" + accId);
+ sf5.setValue("Parent", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("Parent", "transcript:" + accId);
+ sf6.setValue("Parent", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,