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  1. Project Clover database Thu Nov 28 2024 18:06:40 GMT
  2. Package jalview.io

File EmblFlatFileTest.java

 

Code metrics

14
178
7
1
388
272
16
0.09
25.43
7
2.29

Classes

Class Line # Actions
EmblFlatFileTest 49 178 16
0.9899497699%
 

Contributing tests

This file is covered by 6 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.io;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertTrue;
25    import static org.testng.AssertJUnit.assertNotNull;
26    import static org.testng.AssertJUnit.assertNull;
27    import static org.testng.AssertJUnit.assertSame;
28    import static org.testng.AssertJUnit.fail;
29   
30    import java.io.File;
31    import java.io.IOException;
32    import java.net.MalformedURLException;
33    import java.util.Arrays;
34    import java.util.List;
35    import java.util.Set;
36   
37    import org.testng.annotations.BeforeClass;
38    import org.testng.annotations.Test;
39   
40    import jalview.bin.Console;
41    import jalview.datamodel.DBRefEntry;
42    import jalview.datamodel.Mapping;
43    import jalview.datamodel.Sequence.DBModList;
44    import jalview.datamodel.SequenceFeature;
45    import jalview.datamodel.SequenceI;
46    import jalview.datamodel.features.SequenceFeatures;
47    import jalview.util.MapList;
48   
 
49    public class EmblFlatFileTest
50    {
 
51  1 toggle @BeforeClass(alwaysRun = true)
52    public void setUp()
53    {
54  1 Console.initLogger();
55    }
56   
57    /**
58    * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
59    * one of them reverse strand
60    *
61    * @throws MalformedURLException
62    * @throws IOException
63    */
 
64  1 toggle @Test(groups = "Functional")
65    public void testParse() throws MalformedURLException, IOException
66    {
67  1 File dataFile = new File("test/jalview/io/J03321.embl.txt");
68  1 FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
69  1 EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
70  1 List<SequenceI> seqs = parser.getSeqs();
71   
72  1 assertEquals(seqs.size(), 1);
73  1 SequenceI seq = seqs.get(0);
74  1 assertEquals(seq.getName(), "EmblTest|J03321");
75  1 assertEquals(seq.getLength(), 7502);
76  1 assertEquals(seq.getDescription(),
77    "Chlamydia trachomatis plasmid pCHL1, complete sequence");
78   
79    /*
80    * should be 9 CDS features (one is a 'join' of two exons)
81    */
82  1 Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
83  1 assertEquals(featureTypes.size(), 1);
84  1 assertTrue(featureTypes.contains("CDS"));
85   
86    /*
87    * inspect some features (sorted just for convenience of test assertions)
88    */
89  1 List<SequenceFeature> features = seq.getFeatures()
90    .getAllFeatures("CDS");
91  1 SequenceFeatures.sortFeatures(features, true);
92  1 assertEquals(features.size(), 9);
93   
94  1 SequenceFeature sf = features.get(0);
95  1 assertEquals(sf.getBegin(), 1);
96  1 assertEquals(sf.getEnd(), 437);
97  1 assertEquals(sf.getDescription(),
98    "Exon 2 for protein EMBLCDS:AAA91567.1");
99  1 assertEquals(sf.getFeatureGroup(), "EmblTest");
100  1 assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
101  1 assertEquals(sf.getPhase(), "0");
102  1 assertEquals(sf.getStrand(), 1);
103  1 assertEquals(sf.getValue("note"), "pGP7-D");
104    // this is the second exon of circular CDS!
105  1 assertEquals(sf.getValue("exon number"), 2);
106  1 assertEquals(sf.getValue("product"), "hypothetical protein");
107  1 assertEquals(sf.getValue("transl_table"), "11");
108   
109  1 sf = features.get(1);
110  1 assertEquals(sf.getBegin(), 488);
111  1 assertEquals(sf.getEnd(), 1480);
112  1 assertEquals(sf.getDescription(),
113    "Exon 1 for protein EMBLCDS:AAA91568.1");
114  1 assertEquals(sf.getFeatureGroup(), "EmblTest");
115  1 assertEquals(sf.getEnaLocation(), "complement(488..1480)");
116  1 assertEquals(sf.getPhase(), "0");
117  1 assertEquals(sf.getStrand(), -1); // reverse strand!
118  1 assertEquals(sf.getValue("note"), "pGP8-D");
119  1 assertEquals(sf.getValue("exon number"), 1);
120  1 assertEquals(sf.getValue("product"), "hypothetical protein");
121   
122  1 sf = features.get(7);
123  1 assertEquals(sf.getBegin(), 6045);
124  1 assertEquals(sf.getEnd(), 6788);
125  1 assertEquals(sf.getDescription(),
126    "Exon 1 for protein EMBLCDS:AAA91574.1");
127  1 assertEquals(sf.getFeatureGroup(), "EmblTest");
128  1 assertEquals(sf.getEnaLocation(), "6045..6788");
129  1 assertEquals(sf.getPhase(), "0");
130  1 assertEquals(sf.getStrand(), 1);
131  1 assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
132  1 assertEquals(sf.getValue("exon number"), 1);
133  1 assertEquals(sf.getValue("product"), "hypothetical protein");
134   
135    /*
136    * CDS at 7022-7502 is the first exon of the circular CDS
137    */
138  1 sf = features.get(8);
139  1 assertEquals(sf.getBegin(), 7022);
140  1 assertEquals(sf.getEnd(), 7502);
141  1 assertEquals(sf.getDescription(),
142    "Exon 1 for protein EMBLCDS:AAA91567.1");
143  1 assertEquals(sf.getFeatureGroup(), "EmblTest");
144  1 assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
145  1 assertEquals(sf.getPhase(), "0");
146  1 assertEquals(sf.getStrand(), 1);
147  1 assertEquals(sf.getValue("note"), "pGP7-D");
148  1 assertEquals(sf.getValue("exon number"), 1);
149  1 assertEquals(sf.getValue("product"), "hypothetical protein");
150   
151    /*
152    * Verify DBRefs, whether declared in the file or added by Jalview.
153    * There are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries
154    * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
155    * Sample a few here. Note DBRefEntry constructor capitalises source.
156    */
157  1 List<DBRefEntry> dbrefs = seq.getDBRefs();
158  1 assertEquals(dbrefs.size(), 32);
159    // xref to 'self':
160  1 DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
161  1 int[] range = new int[] { 1, seq.getLength() };
162  1 selfRef.setMap(new Mapping(null, range, range, 1, 1));
163  1 assertTrue(dbrefs.contains(selfRef));
164   
165    // 1st DR line; note trailing period is removed
166  1 assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
167    "d4c4942a634e3df4995fd5ac75c26a61")));
168    // the 4th DR line:
169  1 assertTrue(
170    dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941")));
171    // from the first CDS feature
172  1 assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
173    // from the last CDS feature
174  1 assertTrue(
175    dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350")));
176   
177    /*
178    * verify mappings to, and sequences for, UNIPROT proteins
179    */
180  1 int uniprotCount = 0;
181  1 List<int[]> ranges;
182  1 for (DBRefEntry dbref : dbrefs)
183    {
184  32 if ("UNIPROT".equals(dbref.getSource()))
185    {
186  8 uniprotCount++;
187  8 Mapping mapping = dbref.getMap();
188  8 assertNotNull(mapping);
189  8 MapList map = mapping.getMap();
190  8 String mappedToName = mapping.getTo().getName();
191  8 if ("UNIPROT|P0CE16".equals(mappedToName))
192    {
193  1 assertEquals((ranges = map.getFromRanges()).size(), 1);
194  1 assertEquals(ranges.get(0)[0], 1579);
195  1 assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
196  1 assertEquals((ranges = map.getToRanges()).size(), 1);
197  1 assertEquals(ranges.get(0)[0], 1);
198  1 assertEquals(ranges.get(0)[1], 451);
199    // CDS /product carries over as protein product description
200  1 assertEquals(mapping.getTo().getDescription(),
201    "hypothetical protein");
202    }
203  7 else if ("UNIPROT|P0CE17".equals(mappedToName))
204    {
205  1 assertEquals((ranges = map.getFromRanges()).size(), 1);
206  1 assertEquals(ranges.get(0)[0], 2928);
207  1 assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
208  1 assertEquals((ranges = map.getToRanges()).size(), 1);
209  1 assertEquals(ranges.get(0)[0], 1);
210  1 assertEquals(ranges.get(0)[1], 354);
211    }
212  6 else if ("UNIPROT|P0CE18".equals(mappedToName))
213    {
214  1 assertEquals((ranges = map.getFromRanges()).size(), 1);
215  1 assertEquals(ranges.get(0)[0], 4054);
216  1 assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
217  1 assertEquals((ranges = map.getToRanges()).size(), 1);
218  1 assertEquals(ranges.get(0)[0], 1);
219  1 assertEquals(ranges.get(0)[1], 264);
220    }
221  5 else if ("UNIPROT|P0CE19".equals(mappedToName))
222    {
223    // join(7022..7502,1..437)
224  1 assertEquals((ranges = map.getFromRanges()).size(), 2);
225  1 assertEquals(ranges.get(0)[0], 7022);
226  1 assertEquals(ranges.get(0)[1], 7502);
227  1 assertEquals(ranges.get(1)[0], 1);
228  1 assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
229  1 assertEquals((ranges = map.getToRanges()).size(), 1);
230  1 assertEquals(ranges.get(0)[0], 1);
231  1 assertEquals(ranges.get(0)[1], 305);
232    }
233  4 else if ("UNIPROT|P0CE20".equals(mappedToName))
234    {
235    // complement(488..1480)
236  1 assertEquals((ranges = map.getFromRanges()).size(), 1);
237  1 assertEquals(ranges.get(0)[0], 1480);
238  1 assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
239  1 assertEquals((ranges = map.getToRanges()).size(), 1);
240  1 assertEquals(ranges.get(0)[0], 1);
241  1 assertEquals(ranges.get(0)[1], 330);
242    }
243  3 else if (!"UNIPROT|P0CE23".equals(mappedToName)
244    && !"UNIPROT|P10559".equals(mappedToName)
245    && !"UNIPROT|P10560".equals(mappedToName))
246    {
247  0 fail("Unexpected UNIPROT dbref to " + mappedToName);
248    }
249    }
250    }
251  1 assertEquals(uniprotCount, 8);
252    }
253   
254    /**
255    * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
256    * one of them reverse strand
257    *
258    * @throws MalformedURLException
259    * @throws IOException
260    */
 
261  1 toggle @Test(groups = "Functional")
262    public void testParseToRNA() throws MalformedURLException, IOException
263    {
264  1 File dataFile = new File("test/jalview/io/J03321_rna.embl.txt");
265  1 FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
266  1 EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
267  1 List<SequenceI> seqs = parser.getSeqs();
268  1 assertTrue(seqs.get(0).getSequenceAsString().indexOf("u") > -1);
269    }
270   
 
271  1 toggle @Test(groups = "Functional")
272    public void testParse_codonStartNot1()
273    {
274    // TODO verify CDS-to-protein mapping for CDS with /codon_start=2
275    // example: https://www.ebi.ac.uk/ena/browser/api/embl/EU498516
276    }
277   
278    /**
279    * Test for the case that the EMBL CDS has no UNIPROT xref. In this case
280    * Jalview should synthesize an xref to EMBLCDSPROTEIN in the hope this will
281    * allow Get Cross-References.
282    *
283    * @throws IOException
284    */
 
285  1 toggle @Test(groups = "Functional")
286    public void testParse_noUniprotXref() throws IOException
287    {
288    // MN908947 cut down to 40BP, one CDS, length 5 peptide for test purposes
289    // plus an additional (invented) test case:
290    // - multi-line /product qualifier including escaped quotes
291  1 String data = "ID MN908947; SV 3; linear; genomic RNA; STD; VRL; 20 BP.\n"
292    + "DE Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,\n"
293    + "FT CDS 3..17\n"
294    + "FT /protein_id=\"QHD43415.1\"\n"
295    + "FT /product=\"orf1ab polyprotein\n"
296    + "FT \"\"foobar\"\" \"\n"
297    + "FT /translation=\"MRKLD\n"
298    + "SQ Sequence 7496 BP; 2450 A; 1290 C; 1434 G; 2322 T; 0 other;\n"
299    + " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n";
300  1 FileParse fp = new FileParse(data, DataSourceType.PASTE);
301  1 EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
302  1 List<SequenceI> seqs = parser.getSeqs();
303  1 assertEquals(seqs.size(), 1);
304  1 SequenceI seq = seqs.get(0);
305  1 DBModList<DBRefEntry> dbrefs = seq.getDBRefs();
306   
307    /*
308    * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
309    */
310  1 assertEquals(dbrefs.size(), 2);
311   
312    // dbref to self
313  1 DBRefEntry dbref = dbrefs.get(0);
314  1 assertEquals(dbref.getSource(), "EMBLTEST");
315  1 assertEquals(dbref.getAccessionId(), "MN908947");
316  1 Mapping mapping = dbref.getMap();
317  1 assertNull(mapping.getTo());
318  1 MapList map = mapping.getMap();
319  1 assertEquals(map.getFromLowest(), 1);
320  1 assertEquals(map.getFromHighest(), 40);
321  1 assertEquals(map.getToLowest(), 1);
322  1 assertEquals(map.getToHighest(), 40);
323  1 assertEquals(map.getFromRatio(), 1);
324  1 assertEquals(map.getToRatio(), 1);
325   
326    // dbref to inferred EMBLCDSPROTEIN:
327  1 dbref = dbrefs.get(1);
328  1 assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
329  1 assertEquals(dbref.getAccessionId(), "QHD43415.1");
330  1 mapping = dbref.getMap();
331  1 SequenceI mapTo = mapping.getTo();
332  1 assertEquals(mapTo.getName(), "QHD43415.1");
333    // the /product qualifier transfers to protein product description
334  1 assertEquals(mapTo.getDescription(), "orf1ab polyprotein \"foobar\"");
335  1 assertEquals(mapTo.getSequenceAsString(), "MRKLD");
336  1 map = mapping.getMap();
337  1 assertEquals(map.getFromLowest(), 3);
338  1 assertEquals(map.getFromHighest(), 17);
339  1 assertEquals(map.getToLowest(), 1);
340  1 assertEquals(map.getToHighest(), 5);
341  1 assertEquals(map.getFromRatio(), 3);
342  1 assertEquals(map.getToRatio(), 1);
343    }
344   
 
345  1 toggle @Test(groups = "Functional")
346    public void testAdjustForProteinLength()
347    {
348  1 int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
349   
350    // exact length match:
351  1 assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
352   
353    // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
354    // match if we assume exons include stop codon not in protein:
355  1 int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
356  1 assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
357   
358    // truncate last exon by 6bp
359  1 truncated = EmblFlatFile.adjustForProteinLength(4, exons);
360  1 assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 32]");
361   
362    // remove last exon and truncate preceding by 1bp (so 3bp in total)
363  1 truncated = EmblFlatFile.adjustForProteinLength(3, exons);
364  1 assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
365   
366    // exact removal of exon case:
367  1 exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
368  1 truncated = EmblFlatFile.adjustForProteinLength(4, exons);
369  1 assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
370   
371    // what if exons are too short for protein?
372  1 truncated = EmblFlatFile.adjustForProteinLength(7, exons);
373  1 assertSame(exons, truncated);
374    }
375   
 
376  1 toggle @Test(groups = "Functional")
377    public void testRemoveQuotes()
378    {
379  1 assertNull(EmblFlatFile.removeQuotes(null));
380  1 assertEquals(EmblFlatFile.removeQuotes("No quotes here"),
381    "No quotes here");
382  1 assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""),
383    "Enclosing quotes");
384  1 assertEquals(
385    EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""),
386    "Escaped \"quotes\" example");
387    }
388    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 28 2024 18:14:23 GMT using coverage data from Thu Nov 28 2024 18:14:06 GMT.
  • OpenClover is free and open-source software.