From 7d455171bbd58d050fc9fc95bffc3a3b0cf60166 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 25 Oct 2018 20:27:16 +0100 Subject: [PATCH 1/1] JAL-3143 unit tests updated for code changes! --- test/jalview/ext/ensembl/EnsemblCdnaTest.java | 26 +++++++------- test/jalview/ext/ensembl/EnsemblCdsTest.java | 22 ++++++------ test/jalview/ext/ensembl/EnsemblGeneTest.java | 44 +++++++++++------------ test/jalview/ext/ensembl/EnsemblGenomeTest.java | 29 +++++++-------- 4 files changed, 61 insertions(+), 60 deletions(-) diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java index c9d8deb..9e9d9a4 100644 --- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java +++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java @@ -79,19 +79,19 @@ public class EnsemblCdnaTest // exon at (start+10000) length 501 SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f, null); - sf.setValue("Parent", "transcript:" + transcriptId); + sf.setValue("Parent", transcriptId); sf.setStrand("-"); genomic.addSequenceFeature(sf); // exon (sub-type) at (start + exon_variant) length 101 sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null); - sf.setValue("Parent", "transcript:" + transcriptId); + sf.setValue("Parent", transcriptId); sf.setStrand("-"); genomic.addSequenceFeature(sf); // exon belonging to a different transcript doesn't count sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null); - sf.setValue("Parent", "transcript:anotherOne"); + sf.setValue("Parent", "anotherOne"); genomic.addSequenceFeature(sf); // transcript feature doesn't count @@ -134,19 +134,19 @@ public class EnsemblCdnaTest // exon at (start+10000) length 501 SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f, null); - sf.setValue("Parent", "transcript:" + transcriptId); + sf.setValue("Parent", transcriptId); sf.setStrand("+"); genomic.addSequenceFeature(sf); // exon (sub-type) at (start + exon_variant) length 101 sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null); - sf.setValue("Parent", "transcript:" + transcriptId); + sf.setValue("Parent", transcriptId); sf.setStrand("+"); genomic.addSequenceFeature(sf); // exon belonging to a different transcript doesn't count sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null); - sf.setValue("Parent", "transcript:anotherOne"); + sf.setValue("Parent", "anotherOne"); genomic.addSequenceFeature(sf); // transcript feature doesn't count @@ -226,14 +226,14 @@ public class EnsemblCdnaTest 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)); // test is not case-sensitive assertTrue(testee.retainFeature(sf, accId.toLowerCase())); // feature with wrong parent is not retained - sf.setValue("Parent", "transcript:XYZ"); + sf.setValue("Parent", "XYZ"); assertFalse(testee.retainFeature(sf, accId)); } @@ -253,30 +253,30 @@ public class EnsemblCdnaTest // exon with wrong parent: not valid SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null); - sf2.setValue("Parent", "transcript:XYZ"); + sf2.setValue("Parent", "XYZ"); seq.addSequenceFeature(sf2); // exon with right parent is valid SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null); - sf3.setValue("Parent", "transcript:" + accId); + sf3.setValue("Parent", accId); seq.addSequenceFeature(sf3); // exon sub-type with right parent is valid SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 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); // CDS not valid: SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f, null); - sf6.setValue("Parent", "transcript:" + accId); + sf6.setValue("Parent", accId); seq.addSequenceFeature(sf6); List sfs = new EnsemblCdna() diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java index a44ab7f..e7574eb 100644 --- a/test/jalview/ext/ensembl/EnsemblCdsTest.java +++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java @@ -78,19 +78,19 @@ public class EnsemblCdsTest // 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 @@ -135,16 +135,16 @@ public class EnsemblCdsTest 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)); } @@ -164,29 +164,29 @@ public class EnsemblCdsTest // 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 sfs = new EnsemblCds().getIdentifyingFeatures(seq, diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java index 446b4f7..8b1e840 100644 --- a/test/jalview/ext/ensembl/EnsemblGeneTest.java +++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java @@ -81,7 +81,7 @@ public class EnsemblGeneTest // 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); @@ -113,7 +113,7 @@ public class EnsemblGeneTest // 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); @@ -146,30 +146,30 @@ public class EnsemblGeneTest // 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(); @@ -196,24 +196,24 @@ public class EnsemblGeneTest 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); @@ -235,28 +235,28 @@ public class EnsemblGeneTest 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 sfs = new EnsemblGene() diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java index 72ee492..11140f9 100644 --- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java +++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java @@ -77,13 +77,13 @@ public class EnsemblGenomeTest // transcript at (start+10000) length 501 SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null); - sf.setValue("ID", "transcript:" + transcriptId); + sf.setValue("id", transcriptId); sf.setStrand("+"); genomic.addSequenceFeature(sf); // transcript (sub-type) at (start + 10500) length 101 sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null); - sf.setValue("ID", "transcript:" + transcriptId); + sf.setValue("id", transcriptId); sf.setStrand("+"); genomic.addSequenceFeature(sf); @@ -91,13 +91,13 @@ public class EnsemblGenomeTest // although strictly it is a sequence_variant in SO sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000, 0f, null); - sf.setValue("ID", "transcript:" + transcriptId); + sf.setValue("id", transcriptId); sf.setStrand("+"); genomic.addSequenceFeature(sf); // transcript with a different ID doesn't count sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null); - sf.setValue("ID", "transcript:anotherOne"); + sf.setValue("id", "anotherOne"); genomic.addSequenceFeature(sf); // parent of transcript feature doesn't count @@ -150,11 +150,11 @@ public class EnsemblGenomeTest assertTrue(testee.retainFeature(sf, accId)); // other feature with correct parent is kept - sf.setValue("Parent", "transcript:" + accId); + sf.setValue("Parent", accId); assertTrue(testee.retainFeature(sf, accId)); // other feature with wrong parent is not kept - sf.setValue("Parent", "transcript:XYZ"); + sf.setValue("Parent", "XYZ"); assertFalse(testee.retainFeature(sf, accId)); } @@ -174,36 +174,37 @@ public class EnsemblGenomeTest seq.addSequenceFeature(sf1); // transcript with wrong ID not valid - SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f, + // NB change desc to avoid rejection of duplicate feature! + SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f, null); - sf2.setValue("ID", "transcript"); + sf2.setValue("id", "transcript"); seq.addSequenceFeature(sf2); // transcript with right ID is valid - SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f, + SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f, null); - sf3.setValue("ID", "transcript:" + accId); + sf3.setValue("id", accId); seq.addSequenceFeature(sf3); // transcript sub-type with right ID is valid SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null); - sf4.setValue("ID", "transcript:" + accId); + sf4.setValue("id", accId); seq.addSequenceFeature(sf4); // Ensembl treats NMD_transcript_variant as if a transcript SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null); - sf5.setValue("ID", "transcript:" + accId); + sf5.setValue("id", accId); seq.addSequenceFeature(sf5); // gene not valid: SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null); - sf6.setValue("ID", "transcript:" + accId); + sf6.setValue("id", accId); seq.addSequenceFeature(sf6); // exon not valid: SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null); - sf7.setValue("ID", "transcript:" + accId); + sf7.setValue("id", accId); seq.addSequenceFeature(sf7); List sfs = new EnsemblGenome() -- 1.7.10.2