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.assertSame;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.SequenceFeature;
30 import jalview.datamodel.SequenceI;
31 import jalview.datamodel.features.SequenceFeatures;
32 import jalview.gui.JvOptionPane;
33 import jalview.io.DataSourceType;
34 import jalview.io.FastaFile;
35 import jalview.io.gff.SequenceOntologyFactory;
36 import jalview.io.gff.SequenceOntologyLite;
38 import java.lang.reflect.Method;
39 import java.util.Arrays;
40 import java.util.List;
42 import org.testng.Assert;
43 import org.testng.annotations.AfterClass;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.DataProvider;
46 import org.testng.annotations.Test;
48 public class EnsemblSeqProxyTest
51 @BeforeClass(alwaysRun = true)
52 public void setUpJvOptionPane()
54 JvOptionPane.setInteractiveMode(false);
55 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
58 private static final Object[][] allSeqs = new Object[][] {
63 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
64 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
65 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
66 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
67 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
68 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
69 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
70 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
71 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
72 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
73 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
74 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
75 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
80 + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
81 + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
82 + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
83 + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
84 + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
85 + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
86 + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
87 + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
88 + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
89 + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
90 + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
91 + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
92 + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
93 + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
94 + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
95 + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
96 + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
97 + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
98 + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
99 + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
100 + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
101 + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
102 + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
103 + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
104 + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
105 + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
106 + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
107 + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
108 + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
109 + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
110 + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
111 + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
112 + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
113 + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
114 + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
115 + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
116 + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
117 + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
118 + "GGTGCGTTTCCTGTCCACTGA\n" },
120 new EnsemblProtein(),
123 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
124 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
125 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
126 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
127 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
128 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
129 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
130 // ? insertion added in ENSP00000288602.11, not in P15056
131 + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
133 + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
134 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
135 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
136 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
137 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
138 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
139 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
141 @BeforeClass(alwaysRun = true)
144 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
147 @AfterClass(alwaysRun = true)
148 public void tearDown()
150 SequenceOntologyFactory.setInstance(null);
153 @DataProvider(name = "ens_seqs")
154 public Object[][] createData(Method m)
156 System.out.println(m.getName());
160 @Test(dataProvider = "ens_seqs", suiteName = "live")
161 public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
162 String fastasq) throws Exception
164 FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
165 SequenceI[] expected = trueRes.getSeqsAsArray();
166 AlignmentI retrieved = proxy.getSequenceRecords(sq);
168 Assert.assertEquals(retrieved.getHeight(), expected.length,
169 "Different number of sequences retrieved for query " + sq);
171 for (SequenceI tr : expected)
174 Assert.assertNotNull(
175 rseq = retrieved.findSequenceMatch(tr.getName()),
176 "Couldn't find sequences matching expected sequence "
178 Assert.assertEquals(rseq.length, 1,
179 "Expected only one sequence for sequence ID " + tr.getName());
181 rseq[0].getSequenceAsString(),
182 tr.getSequenceAsString(),
183 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
184 + tr.getSequenceAsString() + "\n" + "Got:"
185 + rseq[0].getSequenceAsString());
189 @Test(groups = "Functional")
190 public void getGenomicRangesFromFeatures()
196 * Test the method that appends a single allele's reverse complement to a
199 @Test(groups = "Functional")
200 public void testReverseComplementAllele()
202 StringBuilder sb = new StringBuilder();
203 EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
204 EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
205 EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
206 EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
207 EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
208 assertEquals("C,c,G,A,T", sb.toString());
210 sb = new StringBuilder();
211 EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
212 EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
213 EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
214 assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
218 * Test the method that computes the reverse complement of the alleles in a
219 * sequence_variant feature
221 @Test(groups = "Functional")
222 public void testReverseComplementAlleles()
224 String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
225 SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
227 sf.setValue("alleles", alleles);
228 sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
230 EnsemblSeqProxy.reverseComplementAlleles(sf);
231 String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
232 // verify description is updated with reverse complement
233 assertEquals(revcomp, sf.getDescription());
234 // verify alleles attribute is updated with reverse complement
235 assertEquals(revcomp, sf.getValue("alleles"));
236 // verify attributes string is updated with reverse complement
237 assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
240 @Test(groups = "Functional")
241 public void testSortFeatures()
243 SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
244 SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
245 SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
246 SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
247 List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
250 // sort by start position ascending (forward strand)
251 // sf2 and sf3 tie and should not be reordered by sorting
252 SequenceFeatures.sortFeatures(sfs, true);
253 assertSame(sfs.get(0), sf2);
254 assertSame(sfs.get(1), sf3);
255 assertSame(sfs.get(2), sf1);
256 assertSame(sfs.get(3), sf4);
258 // sort by end position descending (reverse strand)
259 SequenceFeatures.sortFeatures(sfs, false);
260 assertSame(sfs.get(0), sf1);
261 assertSame(sfs.get(1), sf3);
262 assertSame(sfs.get(2), sf2);
263 assertSame(sfs.get(3), sf4);