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.DataProvider;
25 import org.testng.annotations.Test;
28 public class EnsemblSeqProxyTest
30 private static final Object[][] allSeqs = new Object[][] {
35 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
36 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
37 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
38 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
39 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
40 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
41 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
42 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
43 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
44 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
45 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
46 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
47 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
52 + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
53 + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
54 + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
55 + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
56 + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
57 + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
58 + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
59 + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
60 + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
61 + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
62 + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
63 + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
64 + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
65 + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
66 + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
67 + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
68 + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
69 + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
70 + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
71 + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
72 + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
73 + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
74 + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
75 + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
76 + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
77 + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
78 + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
79 + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
80 + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
81 + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
82 + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
83 + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
84 + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
85 + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
86 + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
87 + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
88 + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
89 + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
90 + "GGTGCGTTTCCTGTCCACTGA\n" },
95 + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
96 + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
97 + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
98 + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
99 + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
100 + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
101 + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
102 + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
103 + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
104 + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
105 + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
106 + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
107 + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
109 @DataProvider(name = "queries")
110 public Object[][] createQueryData(Method m)
112 return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
115 @Test(dataProvider = "queries")
116 public void testIsValidReference(String query) throws Exception
118 EnsemblSequenceFetcher esq = new EnsemblProtein();
119 Assert.assertTrue(esq.isValidReference(query),
120 "Expected reference string " + query
121 + " to be valid for regex "
122 + esq.getAccessionValidator().toString());
125 @DataProvider(name = "ens_seqs")
126 public Object[][] createData(Method m)
128 System.out.println(m.getName());
132 @Test(dataProvider = "ens_seqs", suiteName = "live")
133 public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
136 FileParse fp = proxy.getSequenceReader(Arrays
139 SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
140 FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
141 SequenceI[] trueSqs = trueRes.getSeqsAsArray();
142 Assert.assertEquals(sqs.length, trueSqs.length,
143 "Different number of sequences retrieved for query " + sq);
144 Alignment ral = new Alignment(sqs);
145 for (SequenceI tr : trueSqs)
148 Assert.assertNotNull(
149 rseq = ral.findSequenceMatch(tr.getName()),
150 "Couldn't find sequences matching expected sequence "
152 Assert.assertEquals(rseq.length, 1,
153 "Expected only one sequence for sequence ID " + tr.getName());
155 rseq[0].getSequenceAsString(),
156 tr.getSequenceAsString(),
157 "Sequences differ for " + tr.getName() + "\n" + "Exp:"
158 + tr.getSequenceAsString() + "\n" + "Got:"
159 + rseq[0].getSequenceAsString());
164 @Test(suiteName = "live")
165 public void testLiveCheckEnsembl()
167 EnsemblRestClient sf = new EnsemblRestClient()
171 public String getDbName()
173 // TODO Auto-generated method stub
178 public AlignmentI getSequenceRecords(String queries) throws Exception
180 // TODO Auto-generated method stub
185 protected URL getUrl(List<String> ids) throws MalformedURLException
187 // TODO Auto-generated method stub
192 protected boolean useGetRequest()
194 // TODO Auto-generated method stub
199 protected String getRequestMimeType(boolean b)
201 // TODO Auto-generated method stub
206 protected String getResponseMimeType()
208 // TODO Auto-generated method stub
213 boolean isAvailable = sf.isEnsemblAvailable();
214 System.out.println("Ensembl is "
215 + (isAvailable ? "UP!"
216 : "DOWN or unreachable ******************* BAD!"));
220 * Tests for the method that computes all peptide variants given codon
223 @Test(groups = "Functional")
224 public void testComputePeptideVariants()
226 String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
229 * AGT codes for S - this is not included in the variants returned
231 List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
232 assertEquals("[]", variants.toString());
234 // S is reported if it differs from the current value (A):
235 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
236 assertEquals("[S]", variants.toString());
239 * synonymous variant is not reported
241 codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
242 // AGC and AGT both code for S
243 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
244 assertEquals("[]", variants.toString());
247 * equivalent variants are only reported once
249 codonVariants = new String[][] { { "C" }, { "T" },
250 { "A", "C", "G", "T" } };
251 // CTA CTC CTG CTT all code for L
252 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
253 assertEquals("[L]", variants.toString());
256 * vary codons 1 and 2; variant products are sorted and non-redundant
258 codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
259 // aga ata cga cta code for R, I, R, L
260 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
261 assertEquals("[I, L, R]", variants.toString());
264 * vary codons 2 and 3
266 codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
267 // aga agc ata atc code for R, S, I, I
268 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
269 assertEquals("[I, R]", variants.toString());
272 * vary codons 1 and 3
274 codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
275 // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
276 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
277 assertEquals("[K, N, Y, STOP]", variants.toString());
280 * vary codons 1, 2 and 3
282 codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
284 // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
285 variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
286 assertEquals("[C, R, T, W]", variants.toString());
290 * Tests for the method that maps the subset of a dna sequence that has CDS
291 * (or subtype) feature.
293 @Test(groups = "Functional")
294 public void testGetCdsRanges()
296 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
298 SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
299 dnaSeq.createDatasetSequence();
300 SequenceI ds = dnaSeq.getDatasetSequence();
303 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
304 ds.addSequenceFeature(sf);
305 // exon feature should be ignored here
306 sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
307 ds.addSequenceFeature(sf);
309 sf = new SequenceFeature("some_cds", "", 10, 12, 0f, null);
310 ds.addSequenceFeature(sf);
312 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
313 List<int[]> ranges = new ArrayList<int[]>();
314 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
315 assertEquals(6, mappedLength);
316 assertEquals(2, ranges.size());
317 assertEquals(4, ranges.get(0)[0]);
318 assertEquals(6, ranges.get(0)[1]);
319 assertEquals(10, ranges.get(1)[0]);
320 assertEquals(12, ranges.get(1)[1]);
324 @Test(groups = "Functional")
325 public void getGenomicRangesFromFeatures()
331 * Tests for the method that maps the subset of a dna sequence that has CDS
332 * (or subtype) feature - case where the start codon is incomplete.
334 @Test(groups = "Functional")
335 public void testGetCdsRanges_fivePrimeIncomplete()
337 EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
339 SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
340 dnaSeq.createDatasetSequence();
341 SequenceI ds = dnaSeq.getDatasetSequence();
343 // CDS for dna 5-6 (incomplete codon), 7-9
344 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
345 sf.setPhase("2"); // skip 2 bases to start of next codon
346 ds.addSequenceFeature(sf);
347 ds.addSequenceFeature(sf);
349 sf = new SequenceFeature("some_cds", "", 13, 15, 0f, null);
350 ds.addSequenceFeature(sf);
352 SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
353 List<int[]> ranges = new ArrayList<int[]>();
354 int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
357 * check the mapping starts with the first complete codon
359 assertEquals(6, mappedLength);
360 assertEquals(2, ranges.size());
361 assertEquals(7, ranges.get(0)[0]);
362 assertEquals(9, ranges.get(0)[1]);
363 assertEquals(13, ranges.get(1)[0]);
364 assertEquals(15, ranges.get(1)[1]);