2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.ensembl;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
26 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.SequenceFeature;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.FastaFile;
33 import jalview.io.FileParse;
34 import jalview.io.gff.SequenceOntologyFactory;
35 import jalview.io.gff.SequenceOntologyLite;
37 import java.lang.reflect.Method;
38 import java.util.Arrays;
40 import org.testng.Assert;
41 import org.testng.annotations.AfterClass;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.DataProvider;
44 import org.testng.annotations.Test;
46 public class EnsemblSeqProxyTest
48 private static final Object[][] allSeqs = new Object[][] {
53 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
54 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
55 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
56 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
57 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
58 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
59 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
60 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
61 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
62 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
63 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
64 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
65 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
70 + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
71 + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
72 + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
73 + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
74 + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
75 + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
76 + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
77 + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
78 + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
79 + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
80 + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
81 + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
82 + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
83 + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
84 + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
85 + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
86 + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
87 + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
88 + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
89 + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
90 + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
91 + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
92 + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
93 + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
94 + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
95 + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
96 + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
97 + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
98 + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
99 + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
100 + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
101 + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
102 + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
103 + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
104 + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
105 + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
106 + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
107 + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
108 + "GGTGCGTTTCCTGTCCACTGA\n" },
110 new EnsemblProtein(),
113 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
114 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
115 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
116 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
117 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
118 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
119 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
120 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
121 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
122 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
123 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
124 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
125 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
127 @BeforeClass(alwaysRun = true)
130 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
133 @AfterClass(alwaysRun = true)
134 public void tearDown()
136 SequenceOntologyFactory.setInstance(null);
139 @DataProvider(name = "ens_seqs")
140 public Object[][] createData(Method m)
142 System.out.println(m.getName());
146 @Test(dataProvider = "ens_seqs", suiteName = "live")
147 public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
148 String fastasq) throws Exception
150 FileParse fp = proxy.getSequenceReader(Arrays
151 .asList(new String[] { sq }));
152 SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
153 FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
154 SequenceI[] trueSqs = trueRes.getSeqsAsArray();
155 Assert.assertEquals(sqs.length, trueSqs.length,
156 "Different number of sequences retrieved for query " + sq);
157 Alignment ral = new Alignment(sqs);
158 for (SequenceI tr : trueSqs)
161 Assert.assertNotNull(
162 rseq = ral.findSequenceMatch(tr.getName()),
163 "Couldn't find sequences matching expected sequence "
165 Assert.assertEquals(rseq.length, 1,
166 "Expected only one sequence for sequence ID " + tr.getName());
168 rseq[0].getSequenceAsString(),
169 tr.getSequenceAsString(),
170 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
171 + tr.getSequenceAsString() + "\n" + "Got:"
172 + rseq[0].getSequenceAsString());
177 @Test(groups = "Functional")
178 public void getGenomicRangesFromFeatures()
183 @Test(groups = "Functional")
184 public void testIsTranscriptIdentifier()
186 EnsemblSeqProxy testee = new EnsemblGene();
187 assertFalse(testee.isTranscriptIdentifier(null));
188 assertFalse(testee.isTranscriptIdentifier(""));
189 assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
190 assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
191 assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
192 assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
193 assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
194 assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
197 @Test(groups = "Functional")
198 public void testIsGeneIdentifier()
200 EnsemblSeqProxy testee = new EnsemblGene();
201 assertFalse(testee.isGeneIdentifier(null));
202 assertFalse(testee.isGeneIdentifier(""));
203 assertFalse(testee.isGeneIdentifier("ENST00000012345"));
204 assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
205 assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
206 assertFalse(testee.isGeneIdentifier("ensg00000012345"));
207 assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
208 assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
212 * Test the method that appends a single allele's reverse complement to a
215 @Test(groups = "Functional")
216 public void testReverseComplementAllele()
218 StringBuilder sb = new StringBuilder();
219 EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
220 EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
221 EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
222 EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
223 EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
224 assertEquals("C,c,G,A,T", sb.toString());
226 sb = new StringBuilder();
227 EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
228 EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
229 EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
230 assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
234 * Test the method that computes the reverse complement of the alleles in a
235 * sequence_variant feature
237 @Test(groups = "Functional")
238 public void testReverseComplementAlleles()
240 String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
241 SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
243 sf.setValue("alleles", alleles);
244 sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
246 EnsemblSeqProxy.reverseComplementAlleles(sf);
247 String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
248 // verify description is updated with reverse complement
249 assertEquals(revcomp, sf.getDescription());
250 // verify alleles attribute is updated with reverse complement
251 assertEquals(revcomp, sf.getValue("alleles"));
252 // verify attributes string is updated with reverse complement
253 assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
256 @Test(groups = "Functional")
257 public void testSortFeatures()
259 SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
260 SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
261 SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
262 SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
263 SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
265 // sort by start position ascending (forward strand)
266 // sf2 and sf3 tie and should not be reordered by sorting
267 EnsemblSeqProxy.sortFeatures(sfs, true);
268 assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
270 // sort by end position descending (reverse strand)
271 EnsemblSeqProxy.sortFeatures(sfs, false);
272 assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);