testsrc/compbio/data/sequence/SequenceUtilTester.java

   1 /*\r
   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
  12  * license notice.\r
  13  */\r
  14 package compbio.data.sequence;\r
  15 \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
  21 \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
  34 \r
  35 import org.testng.annotations.Test;\r
  36 \r
  37 import compbio.metadata.AllTestSuit;\r
  38 import compbio.runner.disorder.Disembl;\r
  39 \r
  40 public class SequenceUtilTester {\r
  41 \r
  42         @Test()\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
  50 \r
  51                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  52                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  53 \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
  58 \r
  59         }\r
  60 \r
  61         @Test()\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
  66         }\r
  67 \r
  68         @Test()\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
  73         }\r
  74 \r
  75         @Test()\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
  83                 AAseq += "XU";\r
  84                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  85 \r
  86         }\r
  87 \r
  88         @Test()\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
  96 \r
  97                 String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
  98                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  99                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 100                                 .cleanProteinSequence(notaSeq)));\r
 101 \r
 102                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
 103                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
 104                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 105                                 .cleanProteinSequence(AAseq)));\r
 106                 AAseq += "XU";\r
 107 \r
 108                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
 109                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 110                                 .cleanProteinSequence(AAseq)));\r
 111         }\r
 112 \r
 113         @Test()\r
 114         public void testReadWriteFasta() {\r
 115 \r
 116                 try {\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
 124                         fio.close();\r
 125                         FileOutputStream fou = new FileOutputStream(\r
 126                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
 127                         SequenceUtil.writeFasta(fou, fseqs);\r
 128                         fou.close();\r
 129                         FileOutputStream fou20 = new FileOutputStream(\r
 130                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 131                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 132                         fou20.close();\r
 133 \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
 140                 }\r
 141         }\r
 142 \r
 143         // Potential Bug :- Sequence names are shortened to 2-3 letters\r
 144         @Test\r
 145         public void testReadFastaWriteClustal() {\r
 146                 \r
 147                 try {\r
 148                         FileInputStream fio = new FileInputStream(\r
 149                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 150                         assertNotNull(fio);\r
 151                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 152                         assertNotNull(fseqs);\r
 153                         fio.close();\r
 154                         \r
 155                         char gapChar = '-';\r
 156                         FileOutputStream fou = new FileOutputStream(\r
 157                                         AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");\r
 158                         SequenceUtil.writeClustal(fou, fseqs, gapChar);\r
 159                         fou.close();\r
 160                         \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                 }\r
 168         }               \r
 169                 \r
 170                         \r
 171 \r
 172                         \r
 173         \r
 174         /**\r
 175          * This test tests the loading of horizontally formatted Jronn output file\r
 176          */\r
 177         @Test\r
 178         public void loadJronnFile() {\r
 179 \r
 180                 FileInputStream fio;\r
 181                 try {\r
 182                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 183                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 184                         assertNotNull(aseqs);\r
 185                         assertEquals(aseqs.size(), 3);\r
 186                         Score aseq = aseqs.get("Foobar");\r
 187                         assertNotNull(aseq);\r
 188                         assertNotNull(aseq.getScores());\r
 189                         // System.out.println(aseq);\r
 190                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 191                         fio.close();\r
 192                 } catch (FileNotFoundException e) {\r
 193                         e.printStackTrace();\r
 194                         fail(e.getLocalizedMessage());\r
 195                 } catch (IOException e) {\r
 196                         e.printStackTrace();\r
 197                         fail(e.getLocalizedMessage());\r
 198                 } catch (UnknownFileFormatException e) {\r
 199                         e.printStackTrace();\r
 200                         fail(e.getLocalizedMessage());\r
 201                 }\r
 202 \r
 203         }\r
 204 \r
 205         enum Trial {\r
 206                 one, two, three\r
 207         };\r
 208 \r
 209         /**\r
 210          * This test tests the loading of horizontally formatted Jronn output file\r
 211          * \r
 212          * First seq\r
 213          * \r
 214          * M 0.86010 0.88512 0.37094\r
 215          * \r
 216          * T 0.79983 0.85864 0.44331\r
 217          * \r
 218          */\r
 219         @SuppressWarnings("unchecked")\r
 220         @Test\r
 221         public void testReadDisemblResults() {\r
 222 \r
 223 \r
 224                 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
 225                 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
 226                 Map<String,Map<String, Float>>  _values=new HashMap<String, Map<String,Float>>();\r
 227                 Map<String, Float> values = new HashMap<String, Float>();\r
 228                 Set<Range> rset;\r
 229                 rset = new HashSet<Range>();\r
 230                 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
 231                 {\r
 232                         rset.add(new Range(se));\r
 233                 }\r
 234                 ranges.put(DisemblResult.COILS.toString(), rset);\r
 235                 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
 236                 rset = new HashSet<Range>();\r
 237                 for (String[] se:new String[][] { { "355","368"}})\r
 238                 {\r
 239                         rset.add(new Range(se));\r
 240                 }\r
 241                 ranges.put(DisemblResult.REM465.toString(), rset);\r
 242                 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
 243                 rset = new HashSet<Range>();\r
 244                 for (String[] se:new String[][] { { "190","204"}})\r
 245                 {\r
 246                         rset.add(new Range(se));\r
 247                 }\r
 248                 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
 249                 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
 250                 _ranges.put("Foobar_dundeefriends", ranges);\r
 251                 _values.put("Foobar_dundeefriends", values);\r
 252                 FileInputStream fio;\r
 253                 try {\r
 254                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 255                                         + "disembl.out");\r
 256                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 257                         assertNotNull(aseqs);\r
 258                         assertEquals(aseqs.size(), 3);\r
 259                         ScoreManager sman = ScoreManager.newInstance(aseqs);\r
 260 \r
 261                         for (String fs : aseqs.keySet()) {\r
 262                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
 263                                                 .contains(fs));\r
 264                                 Set<Score> scores = aseqs.get(fs);\r
 265                                 assertEquals(scores.size(), 3);\r
 266                                 for (Score sc:scores) {\r
 267                                         if (_ranges.containsKey(fs))\r
 268                                         {\r
 269                                         assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
 270                                         assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
 271                                         }\r
 272                                 }\r
 273                         }\r
 274                         fio.close();\r
 275                 } catch (FileNotFoundException e) {\r
 276                         e.printStackTrace();\r
 277                         fail(e.getLocalizedMessage());\r
 278                 } catch (IOException e) {\r
 279                         e.printStackTrace();\r
 280                         fail(e.getLocalizedMessage());\r
 281                 } catch (UnknownFileFormatException e) {\r
 282                         e.printStackTrace();\r
 283                         fail(e.getLocalizedMessage());\r
 284                 }\r
 285         }\r
 286         /**\r
 287          * This test tests the loading of horizontally formatted Jronn output file\r
 288          * \r
 289          * First sequence:\r
 290          * \r
 291          * >Foobar_dundeefriends\r
 292          * \r
 293          * # GlobDoms 2-358, 373-568\r
 294          * \r
 295          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 296          * \r
 297          * # RESIDUE DYDX RAW SMOOTHED\r
 298          * \r
 299          * M 0.0044 -0.2259 -0.2259\r
 300          * \r
 301          * T -0.1308 -0.2170 -0.2170\r
 302          * \r
 303          * ............\r
 304          * \r
 305          * > Second sequence\r
 306          */\r
 307         @SuppressWarnings("unchecked")\r
 308         @Test\r
 309         public void testReadGlobPlotResults() {\r
 310 \r
 311                 FileInputStream fio;\r
 312                 try {\r
 313                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 314                                         + "globplot.out");\r
 315                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 316                         assertNotNull(aseqs);\r
 317                         assertEquals(aseqs.size(), 3);\r
 318 \r
 319                         String fsdf = null;\r
 320                         Set<Score> scores = null;\r
 321                         for (String fs : aseqs.keySet()) {\r
 322                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 323                                         fsdf = fs;\r
 324                                         scores = aseqs.get(fs);\r
 325                                 }\r
 326                                 assertEquals(scores.size(), 5);\r
 327                         }\r
 328 \r
 329                         ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
 330                         sm.writeOut(new PrintWriter(System.out, true));\r
 331 \r
 332                         for (Score score : scores) {\r
 333 \r
 334                                 if (score.getMethod()\r
 335                                                 .equals(GlobProtResult.Disorder.toString())) {\r
 336                                         assertEquals(score.getRanges().size(), 7);\r
 337                                         assertTrue(score.getScores().isEmpty());\r
 338                                 }\r
 339                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 340                                         assertFalse(score.getScores().isEmpty());\r
 341                                         assertTrue(score.getRanges().isEmpty());\r
 342                                 }\r
 343                         }\r
 344                         fio.close();\r
 345                 } catch (FileNotFoundException e) {\r
 346                         e.printStackTrace();\r
 347                         fail(e.getLocalizedMessage());\r
 348                 } catch (IOException e) {\r
 349                         e.printStackTrace();\r
 350                         fail(e.getLocalizedMessage());\r
 351                 } catch (UnknownFileFormatException e) {\r
 352                         e.printStackTrace();\r
 353                         fail(e.getLocalizedMessage());\r
 354                 }\r
 355         }\r
 356 \r
 357         @Test\r
 358         public void testReadIUPredForShortAndLongDisorder() {\r
 359                 try {\r
 360                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
 361                                         AllTestSuit.TEST_DATA_PATH, "out.long"));\r
 362                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 363                         // man.writeOut(new PrintWriter(System.out, true));\r
 364                         assertNotNull(scores);\r
 365                         assertEquals(3, scores.size());\r
 366 \r
 367                         Score score = scores.get("Foobar_dundeefriends");\r
 368                         assertNotNull(score);\r
 369                         assertEquals(0, score.getRanges().size());\r
 370                         assertEquals(568, score.getScores().size());\r
 371                         assertEquals("Long", score.getMethod());\r
 372 \r
 373                         score = scores.get("Foobar");\r
 374                         assertNotNull(score);\r
 375                         assertEquals(0, score.getRanges().size());\r
 376                         assertEquals(481, score.getScores().size());\r
 377                         assertEquals("Long", score.getMethod());\r
 378 \r
 379                         score = scores.get("dundeefriends");\r
 380                         assertNotNull(score);\r
 381                         assertEquals(0, score.getRanges().size());\r
 382                         assertEquals(513, score.getScores().size());\r
 383                         assertEquals("Long", score.getMethod());\r
 384 \r
 385                 } catch (IOException e) {\r
 386                         e.printStackTrace();\r
 387                         fail(e.getLocalizedMessage());\r
 388                 } catch (UnknownFileFormatException e) {\r
 389                         e.printStackTrace();\r
 390                         fail(e.getLocalizedMessage());\r
 391                 }\r
 392         }\r
 393 \r
 394         @Test\r
 395         public void testReadIUPredForGlobDomain() {\r
 396                 try {\r
 397                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
 398                                         AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
 399                         assertNotNull(scores);\r
 400                         assertEquals(2, scores.size());\r
 401                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 402                         // man.writeOut(new PrintWriter(System.out, true));\r
 403                         assertEquals(2, man.getNumberOfSeq());\r
 404                         Score score = scores.get("P53_HUMA");\r
 405                         assertNotNull(score);\r
 406                         assertEquals(2, score.getRanges().size());\r
 407                         assertEquals(0, score.getScores().size());\r
 408                         assertEquals("Glob", score.getMethod());\r
 409 \r
 410                         score = scores.get("Foobar_dundeefriends");\r
 411                         assertEquals(0, score.getRanges().size());\r
 412                 } catch (IOException e) {\r
 413                         e.printStackTrace();\r
 414                         fail(e.getLocalizedMessage());\r
 415                 } catch (UnknownFileFormatException e) {\r
 416                         e.printStackTrace();\r
 417                         fail(e.getLocalizedMessage());\r
 418                 }\r
 419         }\r
 420         @Test\r
 421         public void testReadAAConResults() {\r
 422                 try {\r
 423                         InputStream inStream = new FileInputStream(\r
 424                                         AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 425                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 426                         inStream.close();\r
 427                         assertNotNull(result);\r
 428                         assertEquals(result.size(), 18);\r
 429 \r
 430                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 431                                         + "aacon_result_single.out");\r
 432                         result = SequenceUtil.readAAConResults(inStream);\r
 433                         inStream.close();\r
 434                         assertNotNull(result);\r
 435                         assertEquals(result.size(), 1);\r
 436                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 437                 } catch (IOException e) {\r
 438                         e.printStackTrace();\r
 439                         fail(e.getMessage());\r
 440                 }\r
 441         }\r
 442 }\r
 443 \r