1 package jalview.ext.ensembl;
3 import static org.testng.AssertJUnit.assertEquals;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentI;
7 import jalview.datamodel.Sequence;
8 import jalview.datamodel.SequenceFeature;
9 import jalview.datamodel.SequenceI;
10 import jalview.io.AppletFormatAdapter;
11 import jalview.io.FastaFile;
12 import jalview.io.FileParse;
13 import jalview.io.gff.SequenceOntologyFactory;
14 import jalview.io.gff.SequenceOntologyLite;
16 import java.lang.reflect.Method;
17 import java.net.MalformedURLException;
19 import java.util.ArrayList;
20 import java.util.Arrays;
21 import java.util.List;
23 import org.testng.Assert;
24 import org.testng.annotations.AfterClass;
25 import org.testng.annotations.BeforeClass;
26 import org.testng.annotations.DataProvider;
27 import org.testng.annotations.Test;
30 public class EnsemblSeqProxyTest
32 private static final Object[][] allSeqs = new Object[][] {
37 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
38 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
39 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
40 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
41 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
42 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
43 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
44 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
45 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
46 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
47 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
48 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
49 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
54 + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
55 + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
56 + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
57 + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
58 + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
59 + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
60 + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
61 + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
62 + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
63 + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
64 + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
65 + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
66 + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
67 + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
68 + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
69 + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
70 + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
71 + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
72 + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
73 + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
74 + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
75 + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
76 + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
77 + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
78 + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
79 + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
80 + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
81 + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
82 + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
83 + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
84 + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
85 + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
86 + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
87 + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
88 + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
89 + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
90 + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
91 + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
92 + "GGTGCGTTTCCTGTCCACTGA\n" },
97 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
98 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
99 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
100 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
101 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
102 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
103 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
104 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
105 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
106 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
107 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
108 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
109 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
114 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
118 public void tearDown()
120 SequenceOntologyFactory.setInstance(null);
123 @DataProvider(name = "ens_seqs")
124 public Object[][] createData(Method m)
126 System.out.println(m.getName());
130 @Test(dataProvider = "ens_seqs", suiteName = "live")
131 public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
134 FileParse fp = proxy.getSequenceReader(Arrays
137 SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
138 FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
139 SequenceI[] trueSqs = trueRes.getSeqsAsArray();
140 Assert.assertEquals(sqs.length, trueSqs.length,
141 "Different number of sequences retrieved for query " + sq);
142 Alignment ral = new Alignment(sqs);
143 for (SequenceI tr : trueSqs)
146 Assert.assertNotNull(
147 rseq = ral.findSequenceMatch(tr.getName()),
148 "Couldn't find sequences matching expected sequence "
150 Assert.assertEquals(rseq.length, 1,
151 "Expected only one sequence for sequence ID " + tr.getName());
153 rseq[0].getSequenceAsString(),
154 tr.getSequenceAsString(),
155 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
156 + tr.getSequenceAsString() + "\n" + "Got:"
157 + rseq[0].getSequenceAsString());
162 @Test(suiteName = "live")
163 public void testLiveCheckEnsembl()
165 EnsemblRestClient sf = new EnsemblRestClient()
169 public String getDbName()
171 // TODO Auto-generated method stub
176 public AlignmentI getSequenceRecords(String queries) throws Exception
178 // TODO Auto-generated method stub
183 protected URL getUrl(List<String> ids) throws MalformedURLException
185 // TODO Auto-generated method stub
190 protected boolean useGetRequest()
192 // TODO Auto-generated method stub
197 protected String getRequestMimeType(boolean b)
199 // TODO Auto-generated method stub
204 protected String getResponseMimeType()
206 // TODO Auto-generated method stub
211 boolean isAvailable = sf.isEnsemblAvailable();
212 System.out.println("Ensembl is "
213 + (isAvailable ? "UP!"
214 : "DOWN or unreachable ******************* BAD!"));
218 * Tests for the method that computes all peptide variants given codon
221 @Test(groups = "Functional")
222 public void testComputePeptideVariants()
224 String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
227 * AGT codes for S - this is not included in the variants returned
229 List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
230 assertEquals("[]", variants.toString());
232 // S is reported if it differs from the current value (A):
233 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
234 assertEquals("[S]", variants.toString());
237 * synonymous variant is not reported
239 codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
240 // AGC and AGT both code for S
241 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
242 assertEquals("[]", variants.toString());
245 * equivalent variants are only reported once
247 codonVariants = new String[][] { { "C" }, { "T" },
248 { "A", "C", "G", "T" } };
249 // CTA CTC CTG CTT all code for L
250 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
251 assertEquals("[L]", variants.toString());
254 * vary codons 1 and 2; variant products are sorted and non-redundant
256 codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
257 // aga ata cga cta code for R, I, R, L
258 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
259 assertEquals("[I, L, R]", variants.toString());
262 * vary codons 2 and 3
264 codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
265 // aga agc ata atc code for R, S, I, I
266 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
267 assertEquals("[I, R]", variants.toString());
270 * vary codons 1 and 3
272 codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
273 // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
274 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
275 assertEquals("[K, N, Y, STOP]", variants.toString());
278 * vary codons 1, 2 and 3
280 codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
282 // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
283 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
284 assertEquals("[C, R, T, W]", variants.toString());
288 * Tests for the method that maps the subset of a dna sequence that has CDS
289 * (or subtype) feature.
291 @Test(groups = "Functional")
292 public void testGetCdsRanges()
294 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
296 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
297 dnaSeq.createDatasetSequence();
298 SequenceI ds = dnaSeq.getDatasetSequence();
301 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
302 ds.addSequenceFeature(sf);
303 // exon feature should be ignored here
304 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
305 ds.addSequenceFeature(sf);
307 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
308 ds.addSequenceFeature(sf);
310 List<int[]> ranges = new ArrayList<int[]>();
311 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
312 assertEquals(6, mappedLength);
313 assertEquals(2, ranges.size());
314 assertEquals(4, ranges.get(0)[0]);
315 assertEquals(6, ranges.get(0)[1]);
316 assertEquals(10, ranges.get(1)[0]);
317 assertEquals(12, ranges.get(1)[1]);
321 @Test(groups = "Functional")
322 public void getGenomicRangesFromFeatures()
328 * Tests for the method that maps the subset of a dna sequence that has CDS
329 * (or subtype) feature - case where the start codon is incomplete.
331 @Test(groups = "Functional")
332 public void testGetCdsRanges_fivePrimeIncomplete()
334 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
336 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
337 dnaSeq.createDatasetSequence();
338 SequenceI ds = dnaSeq.getDatasetSequence();
340 // CDS for dna 5-6 (incomplete codon), 7-9
341 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
342 sf.setPhase("2"); // skip 2 bases to start of next codon
343 ds.addSequenceFeature(sf);
344 ds.addSequenceFeature(sf);
346 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
347 ds.addSequenceFeature(sf);
349 List<int[]> ranges = new ArrayList<int[]>();
350 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
353 * check the mapping starts with the first complete codon
355 assertEquals(6, mappedLength);
356 assertEquals(2, ranges.size());
357 assertEquals(7, ranges.get(0)[0]);
358 assertEquals(9, ranges.get(0)[1]);
359 assertEquals(13, ranges.get(1)[0]);
360 assertEquals(15, ranges.get(1)[1]);