1 package jalview.ext.ensembl;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertTrue;
7 import jalview.analysis.AlignmentUtils;
8 import jalview.datamodel.Alignment;
9 import jalview.datamodel.AlignmentI;
10 import jalview.datamodel.SequenceI;
11 import jalview.io.AppletFormatAdapter;
12 import jalview.io.FastaFile;
13 import jalview.io.FileParse;
14 import jalview.io.gff.SequenceOntologyFactory;
15 import jalview.io.gff.SequenceOntologyLite;
17 import java.lang.reflect.Method;
18 import java.net.MalformedURLException;
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!"));
217 @Test(groups = "Functional")
218 public void getGenomicRangesFromFeatures()
223 @Test(groups = "Functional")
224 public void testIsTranscriptIdentifier()
226 EnsemblSeqProxy testee = new EnsemblGene();
227 assertFalse(testee.isTranscriptIdentifier(null));
228 assertFalse(testee.isTranscriptIdentifier(""));
229 assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
230 assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
231 assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
232 assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
233 assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
234 assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
237 @Test(groups = "Functional")
238 public void testIsGeneIdentifier()
240 EnsemblSeqProxy testee = new EnsemblGene();
241 assertFalse(testee.isGeneIdentifier(null));
242 assertFalse(testee.isGeneIdentifier(""));
243 assertFalse(testee.isGeneIdentifier("ENST00000012345"));
244 assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
245 assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
246 assertFalse(testee.isGeneIdentifier("ensg00000012345"));
247 assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
248 assertFalse(testee.isGeneIdentifier("ENSG0000001234"));