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 = "queries")
124 public Object[][] createQueryData(Method m)
126 return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
129 @Test(dataProvider = "queries")
130 public void testIsValidReference(String query) throws Exception
132 EnsemblSequenceFetcher esq = new EnsemblProtein();
133 Assert.assertTrue(esq.isValidReference(query),
134 "Expected reference string " + query
135 + " to be valid for regex "
136 + esq.getAccessionValidator().toString());
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, String fastasq)
150 FileParse fp = proxy.getSequenceReader(Arrays
153 SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
154 FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
155 SequenceI[] trueSqs = trueRes.getSeqsAsArray();
156 Assert.assertEquals(sqs.length, trueSqs.length,
157 "Different number of sequences retrieved for query " + sq);
158 Alignment ral = new Alignment(sqs);
159 for (SequenceI tr : trueSqs)
162 Assert.assertNotNull(
163 rseq = ral.findSequenceMatch(tr.getName()),
164 "Couldn't find sequences matching expected sequence "
166 Assert.assertEquals(rseq.length, 1,
167 "Expected only one sequence for sequence ID " + tr.getName());
169 rseq[0].getSequenceAsString(),
170 tr.getSequenceAsString(),
171 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
172 + tr.getSequenceAsString() + "\n" + "Got:"
173 + rseq[0].getSequenceAsString());
178 @Test(suiteName = "live")
179 public void testLiveCheckEnsembl()
181 EnsemblRestClient sf = new EnsemblRestClient()
185 public String getDbName()
187 // TODO Auto-generated method stub
192 public AlignmentI getSequenceRecords(String queries) throws Exception
194 // TODO Auto-generated method stub
199 protected URL getUrl(List<String> ids) throws MalformedURLException
201 // TODO Auto-generated method stub
206 protected boolean useGetRequest()
208 // TODO Auto-generated method stub
213 protected String getRequestMimeType(boolean b)
215 // TODO Auto-generated method stub
220 protected String getResponseMimeType()
222 // TODO Auto-generated method stub
227 boolean isAvailable = sf.isEnsemblAvailable();
228 System.out.println("Ensembl is "
229 + (isAvailable ? "UP!"
230 : "DOWN or unreachable ******************* BAD!"));
234 * Tests for the method that computes all peptide variants given codon
237 @Test(groups = "Functional")
238 public void testComputePeptideVariants()
240 String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
243 * AGT codes for S - this is not included in the variants returned
245 List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
246 assertEquals("[]", variants.toString());
248 // S is reported if it differs from the current value (A):
249 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
250 assertEquals("[S]", variants.toString());
253 * synonymous variant is not reported
255 codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
256 // AGC and AGT both code for S
257 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
258 assertEquals("[]", variants.toString());
261 * equivalent variants are only reported once
263 codonVariants = new String[][] { { "C" }, { "T" },
264 { "A", "C", "G", "T" } };
265 // CTA CTC CTG CTT all code for L
266 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
267 assertEquals("[L]", variants.toString());
270 * vary codons 1 and 2; variant products are sorted and non-redundant
272 codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
273 // aga ata cga cta code for R, I, R, L
274 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
275 assertEquals("[I, L, R]", variants.toString());
278 * vary codons 2 and 3
280 codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
281 // aga agc ata atc code for R, S, I, I
282 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
283 assertEquals("[I, R]", variants.toString());
286 * vary codons 1 and 3
288 codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
289 // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
290 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
291 assertEquals("[K, N, Y, STOP]", variants.toString());
294 * vary codons 1, 2 and 3
296 codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
298 // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
299 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
300 assertEquals("[C, R, T, W]", variants.toString());
304 * Tests for the method that maps the subset of a dna sequence that has CDS
305 * (or subtype) feature.
307 @Test(groups = "Functional")
308 public void testGetCdsRanges()
310 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
312 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
313 dnaSeq.createDatasetSequence();
314 SequenceI ds = dnaSeq.getDatasetSequence();
317 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
318 ds.addSequenceFeature(sf);
319 // exon feature should be ignored here
320 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
321 ds.addSequenceFeature(sf);
323 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
324 ds.addSequenceFeature(sf);
326 List<int[]> ranges = new ArrayList<int[]>();
327 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
328 assertEquals(6, mappedLength);
329 assertEquals(2, ranges.size());
330 assertEquals(4, ranges.get(0)[0]);
331 assertEquals(6, ranges.get(0)[1]);
332 assertEquals(10, ranges.get(1)[0]);
333 assertEquals(12, ranges.get(1)[1]);
337 @Test(groups = "Functional")
338 public void getGenomicRangesFromFeatures()
344 * Tests for the method that maps the subset of a dna sequence that has CDS
345 * (or subtype) feature - case where the start codon is incomplete.
347 @Test(groups = "Functional")
348 public void testGetCdsRanges_fivePrimeIncomplete()
350 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
352 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
353 dnaSeq.createDatasetSequence();
354 SequenceI ds = dnaSeq.getDatasetSequence();
356 // CDS for dna 5-6 (incomplete codon), 7-9
357 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
358 sf.setPhase("2"); // skip 2 bases to start of next codon
359 ds.addSequenceFeature(sf);
360 ds.addSequenceFeature(sf);
362 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
363 ds.addSequenceFeature(sf);
365 List<int[]> ranges = new ArrayList<int[]>();
366 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
369 * check the mapping starts with the first complete codon
371 assertEquals(6, mappedLength);
372 assertEquals(2, ranges.size());
373 assertEquals(7, ranges.get(0)[0]);
374 assertEquals(9, ranges.get(0)[1]);
375 assertEquals(13, ranges.get(1)[0]);
376 assertEquals(15, ranges.get(1)[1]);