1 package jalview.ext.ensembl;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertTrue;
6 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
8 import jalview.datamodel.Alignment;
9 import jalview.datamodel.SequenceFeature;
10 import jalview.datamodel.SequenceI;
11 import jalview.io.AppletFormatAdapter;
12 import jalview.io.FastaFile;
13 import jalview.io.FileParse;
14 import jalview.io.gff.SequenceOntologyFactory;
15 import jalview.io.gff.SequenceOntologyLite;
17 import java.lang.reflect.Method;
18 import java.util.Arrays;
20 import org.testng.Assert;
21 import org.testng.annotations.AfterClass;
22 import org.testng.annotations.BeforeClass;
23 import org.testng.annotations.DataProvider;
24 import org.testng.annotations.Test;
26 public class EnsemblSeqProxyTest
28 private static final Object[][] allSeqs = new Object[][] {
33 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
34 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
35 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
36 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
37 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
38 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
39 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
40 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
41 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
42 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
43 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
44 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
45 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
50 + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
51 + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
52 + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
53 + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
54 + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
55 + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
56 + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
57 + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
58 + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
59 + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
60 + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
61 + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
62 + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
63 + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
64 + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
65 + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
66 + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
67 + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
68 + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
69 + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
70 + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
71 + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
72 + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
73 + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
74 + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
75 + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
76 + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
77 + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
78 + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
79 + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
80 + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
81 + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
82 + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
83 + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
84 + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
85 + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
86 + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
87 + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
88 + "GGTGCGTTTCCTGTCCACTGA\n" },
93 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
94 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
95 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
96 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
97 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
98 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
99 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
100 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
101 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
102 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
103 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
104 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
105 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
107 @BeforeClass(alwaysRun = true)
110 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
113 @AfterClass(alwaysRun = true)
114 public void tearDown()
116 SequenceOntologyFactory.setInstance(null);
119 @DataProvider(name = "ens_seqs")
120 public Object[][] createData(Method m)
122 System.out.println(m.getName());
126 @Test(dataProvider = "ens_seqs", suiteName = "live")
127 public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
128 String fastasq) throws Exception
130 FileParse fp = proxy.getSequenceReader(Arrays
131 .asList(new String[] { sq }));
132 SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
133 FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
134 SequenceI[] trueSqs = trueRes.getSeqsAsArray();
135 Assert.assertEquals(sqs.length, trueSqs.length,
136 "Different number of sequences retrieved for query " + sq);
137 Alignment ral = new Alignment(sqs);
138 for (SequenceI tr : trueSqs)
141 Assert.assertNotNull(
142 rseq = ral.findSequenceMatch(tr.getName()),
143 "Couldn't find sequences matching expected sequence "
145 Assert.assertEquals(rseq.length, 1,
146 "Expected only one sequence for sequence ID " + tr.getName());
148 rseq[0].getSequenceAsString(),
149 tr.getSequenceAsString(),
150 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
151 + tr.getSequenceAsString() + "\n" + "Got:"
152 + rseq[0].getSequenceAsString());
157 @Test(groups = "Functional")
158 public void getGenomicRangesFromFeatures()
163 @Test(groups = "Functional")
164 public void testIsTranscriptIdentifier()
166 EnsemblSeqProxy testee = new EnsemblGene();
167 assertFalse(testee.isTranscriptIdentifier(null));
168 assertFalse(testee.isTranscriptIdentifier(""));
169 assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
170 assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
171 assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
172 assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
173 assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
174 assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
177 @Test(groups = "Functional")
178 public void testIsGeneIdentifier()
180 EnsemblSeqProxy testee = new EnsemblGene();
181 assertFalse(testee.isGeneIdentifier(null));
182 assertFalse(testee.isGeneIdentifier(""));
183 assertFalse(testee.isGeneIdentifier("ENST00000012345"));
184 assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
185 assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
186 assertFalse(testee.isGeneIdentifier("ensg00000012345"));
187 assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
188 assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
192 * Test the method that appends a single allele's reverse complement to a
195 @Test(groups = "Functional")
196 public void testReverseComplementAllele()
198 StringBuilder sb = new StringBuilder();
199 EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
200 EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
201 EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
202 EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
203 EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
204 assertEquals("C,c,G,A,T", sb.toString());
206 sb = new StringBuilder();
207 EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
208 EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
209 EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
210 assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
214 * Test the method that computes the reverse complement of the alleles in a
215 * sequence_variant feature
217 @Test(groups = "Functional")
218 public void testReverseComplementAlleles()
220 String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
221 SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
223 sf.setValue("alleles", alleles);
224 sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
226 EnsemblSeqProxy.reverseComplementAlleles(sf);
227 String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
228 // verify description is updated with reverse complement
229 assertEquals(revcomp, sf.getDescription());
230 // verify alleles attribute is updated with reverse complement
231 assertEquals(revcomp, sf.getValue("alleles"));
232 // verify attributes string is updated with reverse complement
233 assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
236 @Test(groups = "Functional")
237 public void testSortFeatures()
239 SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
240 SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
241 SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
242 SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
243 SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
245 // sort by start position ascending (forward strand)
246 // sf2 and sf3 tie and should not be reordered by sorting
247 EnsemblSeqProxy.sortFeatures(sfs, true);
248 assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
250 // sort by end position descending (reverse strand)
251 EnsemblSeqProxy.sortFeatures(sfs, false);
252 assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);