2 * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
\r
3 * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
\r
4 * and/or modify it under the terms of the Apache License version 2 as published
\r
5 * by the Apache Software Foundation This library is distributed in the hope
\r
6 * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
\r
7 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
8 * Apache License for more details. A copy of the license is in
\r
9 * apache_license.txt. It is also available here:
\r
10 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
\r
11 * derived work distributed in source code form must include this copyright and
\r
14 package compbio.data.sequence;
\r
16 import static org.testng.AssertJUnit.assertEquals;
\r
17 import static org.testng.AssertJUnit.assertFalse;
\r
18 import static org.testng.AssertJUnit.assertNotNull;
\r
19 import static org.testng.AssertJUnit.assertTrue;
\r
20 import static org.testng.AssertJUnit.fail;
\r
22 import java.io.File;
\r
23 import java.io.FileInputStream;
\r
24 import java.io.FileNotFoundException;
\r
25 import java.io.FileOutputStream;
\r
26 import java.io.IOException;
\r
27 import java.io.InputStream;
\r
28 import java.io.PrintWriter;
\r
29 import java.util.HashMap;
\r
30 import java.util.HashSet;
\r
31 import java.util.List;
\r
32 import java.util.Map;
\r
33 import java.util.Set;
\r
35 import org.testng.annotations.Test;
\r
37 import compbio.metadata.AllTestSuit;
\r
38 import compbio.runner.disorder.Disembl;
\r
40 public class SequenceUtilTester {
\r
43 public void testisNonAmbNucleotideSequence() {
\r
44 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";
\r
45 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));
\r
46 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";
\r
47 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));
\r
48 String nonDna = "atgfctgatgcatgcatgatgctga";
\r
49 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
51 nonDna = "atgc1tgatgcatgcatgatgctga";
\r
52 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
54 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
\r
55 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
56 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code
\r
57 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
62 public void testCleanSequence() {
\r
63 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
\r
64 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
\r
65 SequenceUtil.cleanSequence(dirtySeq));
\r
69 public void testDeepCleanSequence() {
\r
70 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";
\r
71 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
\r
72 SequenceUtil.deepCleanSequence(dirtySeq));
\r
76 public void testisProteinSequence() {
\r
77 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
\r
78 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
\r
79 String notaSeq = "atgc1tgatgcatgcatgatgctga";
\r
80 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
\r
81 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
\r
82 assertTrue(SequenceUtil.isProteinSequence(AAseq));
\r
84 assertFalse(SequenceUtil.isProteinSequence(AAseq));
\r
89 public void testCleanProteinSequence() {
\r
90 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
\r
91 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
\r
92 // This will still be NON protein sequence despite having only correct
\r
93 // letters because the letters match perfectly the nucleotide sequence!
\r
94 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil
\r
95 .cleanProteinSequence(dirtySeq)));
\r
97 String notaSeq = "atgc1tgatgcatgcatgatgmctga";
\r
98 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
\r
99 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
\r
100 .cleanProteinSequence(notaSeq)));
\r
102 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
\r
103 assertTrue(SequenceUtil.isProteinSequence(AAseq));
\r
104 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
\r
105 .cleanProteinSequence(AAseq)));
\r
108 assertFalse(SequenceUtil.isProteinSequence(AAseq));
\r
109 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
\r
110 .cleanProteinSequence(AAseq)));
\r
114 public void testReadWriteFasta() {
\r
117 FileInputStream fio = new FileInputStream(
\r
118 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
\r
119 assertNotNull(fio);
\r
120 List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
\r
121 assertNotNull(fseqs);
\r
122 assertEquals(3, fseqs.size());
\r
123 assertEquals(3, fseqs.size());
\r
125 FileOutputStream fou = new FileOutputStream(
\r
126 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");
\r
127 SequenceUtil.writeFasta(fou, fseqs);
\r
129 FileOutputStream fou20 = new FileOutputStream(
\r
130 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
\r
131 SequenceUtil.writeFasta(fou20, fseqs, 21);
\r
134 } catch (FileNotFoundException e) {
\r
135 e.printStackTrace();
\r
136 fail(e.getLocalizedMessage());
\r
137 } catch (IOException e) {
\r
138 e.printStackTrace();
\r
139 fail(e.getLocalizedMessage());
\r
144 * This test tests the loading of horizontally formatted Jronn output file
\r
147 public void loadJronnFile() {
\r
149 FileInputStream fio;
\r
151 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
\r
152 Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);
\r
153 assertNotNull(aseqs);
\r
154 assertEquals(aseqs.size(), 3);
\r
155 Score aseq = aseqs.get("Foobar");
\r
156 assertNotNull(aseq);
\r
157 assertNotNull(aseq.getScores());
\r
158 // System.out.println(aseq);
\r
159 assertEquals(aseq.getScores().size(), aseq.getScores().size());
\r
161 } catch (FileNotFoundException e) {
\r
162 e.printStackTrace();
\r
163 fail(e.getLocalizedMessage());
\r
164 } catch (IOException e) {
\r
165 e.printStackTrace();
\r
166 fail(e.getLocalizedMessage());
\r
167 } catch (UnknownFileFormatException e) {
\r
168 e.printStackTrace();
\r
169 fail(e.getLocalizedMessage());
\r
179 * This test tests the loading of horizontally formatted Jronn output file
\r
183 * M 0.86010 0.88512 0.37094
\r
185 * T 0.79983 0.85864 0.44331
\r
188 @SuppressWarnings("unchecked")
\r
190 public void testReadDisemblResults() {
\r
193 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();
\r
194 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();
\r
195 Map<String,Map<String, Float>> _values=new HashMap<String, Map<String,Float>>();
\r
196 Map<String, Float> values = new HashMap<String, Float>();
\r
198 rset = new HashSet<Range>();
\r
199 for (String[] se:new String[][] { { "34","41"},{"50","58"},{"83","91"},{"118","127"},{" 160","169"},{" 191","220"},{" 243","252"},{" 287","343"},{" 350","391"},{" 429","485"},{" 497","506"},{"539","547"}})
\r
201 rset.add(new Range(se));
\r
203 ranges.put(DisemblResult.COILS.toString(), rset);
\r
204 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));
\r
205 rset = new HashSet<Range>();
\r
206 for (String[] se:new String[][] { { "355","368"}})
\r
208 rset.add(new Range(se));
\r
210 ranges.put(DisemblResult.REM465.toString(), rset);
\r
211 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));
\r
212 rset = new HashSet<Range>();
\r
213 for (String[] se:new String[][] { { "190","204"}})
\r
215 rset.add(new Range(se));
\r
217 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);
\r
218 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));
\r
219 _ranges.put("Foobar_dundeefriends", ranges);
\r
220 _values.put("Foobar_dundeefriends", values);
\r
221 FileInputStream fio;
\r
223 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
\r
225 Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);
\r
226 assertNotNull(aseqs);
\r
227 assertEquals(aseqs.size(), 3);
\r
228 ScoreManager sman = ScoreManager.newInstance(aseqs);
\r
230 for (String fs : aseqs.keySet()) {
\r
231 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "
\r
233 Set<Score> scores = aseqs.get(fs);
\r
234 assertEquals(scores.size(), 3);
\r
235 for (Score sc:scores) {
\r
236 if (_ranges.containsKey(fs))
\r
238 assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());
\r
239 assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));
\r
244 } catch (FileNotFoundException e) {
\r
245 e.printStackTrace();
\r
246 fail(e.getLocalizedMessage());
\r
247 } catch (IOException e) {
\r
248 e.printStackTrace();
\r
249 fail(e.getLocalizedMessage());
\r
250 } catch (UnknownFileFormatException e) {
\r
251 e.printStackTrace();
\r
252 fail(e.getLocalizedMessage());
\r
256 * This test tests the loading of horizontally formatted Jronn output file
\r
260 * >Foobar_dundeefriends
\r
262 * # GlobDoms 2-358, 373-568
\r
264 * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481
\r
266 * # RESIDUE DYDX RAW SMOOTHED
\r
268 * M 0.0044 -0.2259 -0.2259
\r
270 * T -0.1308 -0.2170 -0.2170
\r
274 * > Second sequence
\r
276 @SuppressWarnings("unchecked")
\r
278 public void testReadGlobPlotResults() {
\r
280 FileInputStream fio;
\r
282 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
\r
284 HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);
\r
285 assertNotNull(aseqs);
\r
286 assertEquals(aseqs.size(), 3);
\r
288 String fsdf = null;
\r
289 Set<Score> scores = null;
\r
290 for (String fs : aseqs.keySet()) {
\r
291 if ("Foobar_dundeefriends".contains(fs)) {
\r
293 scores = aseqs.get(fs);
\r
295 assertEquals(scores.size(), 5);
\r
298 ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);
\r
299 sm.writeOut(new PrintWriter(System.out, true));
\r
301 for (Score score : scores) {
\r
303 if (score.getMethod()
\r
304 .equals(GlobProtResult.Disorder.toString())) {
\r
305 assertEquals(score.getRanges().size(), 7);
\r
306 assertTrue(score.getScores().isEmpty());
\r
308 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {
\r
309 assertFalse(score.getScores().isEmpty());
\r
310 assertTrue(score.getRanges().isEmpty());
\r
314 } catch (FileNotFoundException e) {
\r
315 e.printStackTrace();
\r
316 fail(e.getLocalizedMessage());
\r
317 } catch (IOException e) {
\r
318 e.printStackTrace();
\r
319 fail(e.getLocalizedMessage());
\r
320 } catch (UnknownFileFormatException e) {
\r
321 e.printStackTrace();
\r
322 fail(e.getLocalizedMessage());
\r
327 public void testReadIUPredForShortAndLongDisorder() {
\r
329 Map<String, Score> scores = SequenceUtil.readIUPred(new File(
\r
330 AllTestSuit.TEST_DATA_PATH, "out.long"));
\r
331 ScoreManager man = ScoreManager.newInstanceSingleScore(scores);
\r
332 // man.writeOut(new PrintWriter(System.out, true));
\r
333 assertNotNull(scores);
\r
334 assertEquals(3, scores.size());
\r
336 Score score = scores.get("Foobar_dundeefriends");
\r
337 assertNotNull(score);
\r
338 assertEquals(0, score.getRanges().size());
\r
339 assertEquals(568, score.getScores().size());
\r
340 assertEquals("Long", score.getMethod());
\r
342 score = scores.get("Foobar");
\r
343 assertNotNull(score);
\r
344 assertEquals(0, score.getRanges().size());
\r
345 assertEquals(481, score.getScores().size());
\r
346 assertEquals("Long", score.getMethod());
\r
348 score = scores.get("dundeefriends");
\r
349 assertNotNull(score);
\r
350 assertEquals(0, score.getRanges().size());
\r
351 assertEquals(513, score.getScores().size());
\r
352 assertEquals("Long", score.getMethod());
\r
354 } catch (IOException e) {
\r
355 e.printStackTrace();
\r
356 fail(e.getLocalizedMessage());
\r
357 } catch (UnknownFileFormatException e) {
\r
358 e.printStackTrace();
\r
359 fail(e.getLocalizedMessage());
\r
364 public void testReadIUPredForGlobDomain() {
\r
366 Map<String, Score> scores = SequenceUtil.readIUPred(new File(
\r
367 AllTestSuit.TEST_DATA_PATH, "output.glob"));
\r
368 assertNotNull(scores);
\r
369 assertEquals(2, scores.size());
\r
370 ScoreManager man = ScoreManager.newInstanceSingleScore(scores);
\r
371 // man.writeOut(new PrintWriter(System.out, true));
\r
372 assertEquals(2, man.getNumberOfSeq());
\r
373 Score score = scores.get("P53_HUMA");
\r
374 assertNotNull(score);
\r
375 assertEquals(2, score.getRanges().size());
\r
376 assertEquals(0, score.getScores().size());
\r
377 assertEquals("Glob", score.getMethod());
\r
379 score = scores.get("Foobar_dundeefriends");
\r
380 assertEquals(0, score.getRanges().size());
\r
381 } catch (IOException e) {
\r
382 e.printStackTrace();
\r
383 fail(e.getLocalizedMessage());
\r
384 } catch (UnknownFileFormatException e) {
\r
385 e.printStackTrace();
\r
386 fail(e.getLocalizedMessage());
\r
390 public void testReadAAConResults() {
\r
392 InputStream inStream = new FileInputStream(
\r
393 AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");
\r
394 HashSet<Score> result = SequenceUtil.readAAConResults(inStream);
\r
396 assertNotNull(result);
\r
397 assertEquals(result.size(), 18);
\r
399 inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH
\r
400 + "aacon_result_single.out");
\r
401 result = SequenceUtil.readAAConResults(inStream);
\r
403 assertNotNull(result);
\r
404 assertEquals(result.size(), 1);
\r
405 assertEquals(result.iterator().next().getScores().size(), 568);
\r
406 } catch (IOException e) {
\r
407 e.printStackTrace();
\r
408 fail(e.getMessage());
\r