testsrc/compbio/data/sequence/SequenceUtilTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  * \r
   4  *  JAva Bioinformatics Analysis Web Services (JABAWS) \r
   5  *  @version: 2.5\r
   6  * \r
   7  * This library is free software; you can redistribute it and/or modify it under \r
   8  * the terms of the Apache License version 2 as published\r
   9  * by the Apache Software Foundation This library is distributed in the hope\r
  10  * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
  11  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
  12  * Apache License for more details. A copy of the license is in\r
  13  * apache_license.txt. It is also available here:\r
  14  * \r
  15  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
  16  * \r
  17  * Any republication or derived work distributed in source code form must include \r
  18  * this copyright and license notice.\r
  19  */\r
  20 package compbio.data.sequence;\r
  21 \r
  22 import static org.testng.AssertJUnit.assertEquals;\r
  23 import static org.testng.AssertJUnit.assertFalse;\r
  24 import static org.testng.AssertJUnit.assertNotNull;\r
  25 import static org.testng.AssertJUnit.assertTrue;\r
  26 import static org.testng.AssertJUnit.fail;\r
  27 \r
  28 import java.io.File;\r
  29 import java.io.FileInputStream;\r
  30 import java.io.FileNotFoundException;\r
  31 import java.io.FileOutputStream;\r
  32 import java.io.IOException;\r
  33 import java.io.InputStream;\r
  34 import java.io.PrintWriter;\r
  35 import java.util.HashMap;\r
  36 import java.util.HashSet;\r
  37 import java.util.List;\r
  38 import java.util.Map;\r
  39 import java.util.Set;\r
  40 \r
  41 import org.testng.annotations.Test;\r
  42 \r
  43 import compbio.metadata.AllTestSuit;\r
  44 \r
  45 public class SequenceUtilTester {\r
  46 \r
  47         @Test()\r
  48         public void isNonAmbNucleotideSequence() {\r
  49                 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
  50                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
  51                 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
  52                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
  53                 String nonDna = "atgfctgatgcatgcatgatgctga";\r
  54                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  55 \r
  56                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  57                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  58 \r
  59                 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  60                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  61                 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
  62                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  63         }\r
  64 \r
  65         @Test()\r
  66         public void CleanSequence() {\r
  67                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  68                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.cleanSequence(dirtySeq));\r
  69         }\r
  70 \r
  71         @Test()\r
  72         public void DeepCleanSequence() {\r
  73                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  74                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.deepCleanSequence(dirtySeq));\r
  75         }\r
  76 \r
  77         @Test()\r
  78         public void isProteinSequence() {\r
  79                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  80                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  81                 String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
  82                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  83                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  84                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  85                 AAseq += "XU";\r
  86                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  87 \r
  88         }\r
  89 \r
  90         @Test()\r
  91         public void CleanProteinSequence() {\r
  92                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  93                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  94                 // This will still be NON protein sequence despite having only correct\r
  95                 // letters because the letters match perfectly the nucleotide sequence!\r
  96                 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(dirtySeq)));\r
  97 \r
  98                 String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
  99                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
 100                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(notaSeq)));\r
 101 \r
 102                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
 103                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
 104                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
 105                 AAseq += "XU";\r
 106 \r
 107                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
 108                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
 109         }\r
 110 \r
 111         @Test()\r
 112         public void ReadWriteFasta() {\r
 113                 try {\r
 114                         FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 115                         assertNotNull(fio);\r
 116                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 117                         assertNotNull(fseqs);\r
 118                         assertEquals(3, fseqs.size());\r
 119                         assertEquals(3, fseqs.size());\r
 120                         fio.close();\r
 121                         FileOutputStream fou = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
 122                         SequenceUtil.writeFasta(fou, fseqs);\r
 123                         fou.close();\r
 124                         FileOutputStream fou20 = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 125                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 126                         fou20.close();\r
 127                 } catch (FileNotFoundException e) {\r
 128                         e.printStackTrace();\r
 129                         fail(e.getLocalizedMessage());\r
 130                 } catch (IOException e) {\r
 131                         e.printStackTrace();\r
 132                         fail(e.getLocalizedMessage());\r
 133                 }\r
 134         }\r
 135 \r
 136         // Potential Bug :- Sequence names are shortened to 2-3 letters\r
 137         @Test\r
 138         public void testReadFastaWriteClustal() {\r
 139                 \r
 140                 try {\r
 141                         FileInputStream fio = new FileInputStream(\r
 142                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 143                         assertNotNull(fio);\r
 144                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 145                         assertNotNull(fseqs);\r
 146                         fio.close();\r
 147                         \r
 148                         char gapChar = '-';\r
 149                         FileOutputStream fou = new FileOutputStream(\r
 150                                         AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");\r
 151                         SequenceUtil.writeClustal(fou, fseqs, gapChar);\r
 152                         fou.close();\r
 153                         \r
 154                 } catch (FileNotFoundException e) {\r
 155                         e.printStackTrace();\r
 156                         fail(e.getLocalizedMessage());\r
 157                 } catch (IOException e) {\r
 158                         e.printStackTrace();\r
 159                         fail(e.getLocalizedMessage());\r
 160                 }\r
 161         }\r
 162 \r
 163         /**\r
 164          * This test tests the loading of horizontally formatted Jronn output file\r
 165          */\r
 166         @Test\r
 167         public void LoadJronnFile() {\r
 168 \r
 169                 FileInputStream fio;\r
 170                 try {\r
 171                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 172                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 173                         assertNotNull(aseqs);\r
 174                         assertEquals(aseqs.size(), 3);\r
 175                         Score aseq = aseqs.get("Foobar");\r
 176                         assertNotNull(aseq);\r
 177                         assertNotNull(aseq.getScores());\r
 178                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 179                         fio.close();\r
 180                 } catch (FileNotFoundException e) {\r
 181                         e.printStackTrace();\r
 182                         fail(e.getLocalizedMessage());\r
 183                 } catch (IOException e) {\r
 184                         e.printStackTrace();\r
 185                         fail(e.getLocalizedMessage());\r
 186                 } catch (UnknownFileFormatException e) {\r
 187                         e.printStackTrace();\r
 188                         fail(e.getLocalizedMessage());\r
 189                 }\r
 190         }\r
 191 \r
 192         enum Trial {\r
 193                 one, two, three\r
 194         };\r
 195 \r
 196         /**\r
 197          * This test tests the loading of horizontally formatted Jronn output file\r
 198          * \r
 199          * First seq\r
 200          * \r
 201          * M 0.86010 0.88512 0.37094\r
 202          * \r
 203          * T 0.79983 0.85864 0.44331\r
 204          * \r
 205          */\r
 206         @SuppressWarnings("unchecked")\r
 207         @Test\r
 208         public void ReadDisemblResults() {\r
 209                 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
 210                 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
 211                 Map<String,Map<String, Float>>  _values=new HashMap<String, Map<String,Float>>();\r
 212                 Map<String, Float> values = new HashMap<String, Float>();\r
 213                 Set<Range> rset;\r
 214                 rset = new HashSet<Range>();\r
 215                 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
 216                         rset.add(new Range(se));\r
 217                 }\r
 218                 ranges.put(DisemblResult.COILS.toString(), rset);\r
 219                 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
 220                 rset = new HashSet<Range>();\r
 221                 for (String[] se:new String[][] { { "355","368"}}) {\r
 222                         rset.add(new Range(se));\r
 223                 }\r
 224                 ranges.put(DisemblResult.REM465.toString(), rset);\r
 225                 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
 226                 rset = new HashSet<Range>();\r
 227                 for (String[] se:new String[][] { { "190","204"}}) {\r
 228                         rset.add(new Range(se));\r
 229                 }\r
 230                 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
 231                 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
 232                 _ranges.put("Foobar_dundeefriends", ranges);\r
 233                 _values.put("Foobar_dundeefriends", values);\r
 234                 FileInputStream fio;\r
 235                 try {\r
 236                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "disembl.out");\r
 237                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 238                         assertNotNull(aseqs);\r
 239                         assertEquals(aseqs.size(), 3);\r
 240                         ScoreManager sman = ScoreManager.newInstance(aseqs);\r
 241 \r
 242                         for (String fs : aseqs.keySet()) {\r
 243                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs));\r
 244                                 Set<Score> scores = aseqs.get(fs);\r
 245                                 assertEquals(scores.size(), 3);\r
 246                                 for (Score sc:scores) {\r
 247                                         if (_ranges.containsKey(fs)) {\r
 248                                                 assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
 249                                                 assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
 250                                         }\r
 251                                 }\r
 252                         }\r
 253                         fio.close();\r
 254                 } catch (FileNotFoundException e) {\r
 255                         e.printStackTrace();\r
 256                         fail(e.getLocalizedMessage());\r
 257                 } catch (IOException e) {\r
 258                         e.printStackTrace();\r
 259                         fail(e.getLocalizedMessage());\r
 260                 } catch (UnknownFileFormatException e) {\r
 261                         e.printStackTrace();\r
 262                         fail(e.getLocalizedMessage());\r
 263                 }\r
 264         }\r
 265 \r
 266         /**\r
 267          * This method tests the loading of horizontally formatted Jronn output file\r
 268          * \r
 269          * First sequence:\r
 270          * \r
 271          * >Foobar_dundeefriends\r
 272          * \r
 273          * # GlobDoms 2-358, 373-568\r
 274          * \r
 275          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 276          * \r
 277          * # RESIDUE DYDX RAW SMOOTHED\r
 278          * \r
 279          * M 0.0044 -0.2259 -0.2259\r
 280          * \r
 281          * T -0.1308 -0.2170 -0.2170\r
 282          * \r
 283          * ............\r
 284          * \r
 285          * > Second sequence\r
 286          */\r
 287         @SuppressWarnings("unchecked")\r
 288         @Test\r
 289         public void ReadGlobPlotResults() {\r
 290 \r
 291                 FileInputStream fio;\r
 292                 try {\r
 293                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "globplot.out");\r
 294                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 295                         assertNotNull(aseqs);\r
 296                         assertEquals(aseqs.size(), 3);\r
 297 \r
 298                         String fsdf = null;\r
 299                         Set<Score> scores = null;\r
 300                         for (String fs : aseqs.keySet()) {\r
 301                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 302                                         fsdf = fs;\r
 303                                         scores = aseqs.get(fs);\r
 304                                 }\r
 305                                 assertEquals(scores.size(), 5);\r
 306                         }\r
 307 \r
 308                         ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
 309                         sm.writeOut(new PrintWriter(System.out, true));\r
 310 \r
 311                         for (Score score : scores) {\r
 312                                 if (score.getMethod().equals(GlobProtResult.Disorder.toString())) {\r
 313                                         assertEquals(score.getRanges().size(), 7);\r
 314                                         assertTrue(score.getScores().isEmpty());\r
 315                                 }\r
 316                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 317                                         assertFalse(score.getScores().isEmpty());\r
 318                                         assertTrue(score.getRanges().isEmpty());\r
 319                                 }\r
 320                         }\r
 321                         fio.close();\r
 322                 } catch (FileNotFoundException e) {\r
 323                         e.printStackTrace();\r
 324                         fail(e.getLocalizedMessage());\r
 325                 } catch (IOException e) {\r
 326                         e.printStackTrace();\r
 327                         fail(e.getLocalizedMessage());\r
 328                 } catch (UnknownFileFormatException e) {\r
 329                         e.printStackTrace();\r
 330                         fail(e.getLocalizedMessage());\r
 331                 }\r
 332         }\r
 333 \r
 334         @Test\r
 335         public void ReadIUPredForShortAndLongDisorder() {\r
 336                 try {\r
 337                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "out.long"));\r
 338                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 339                         assertNotNull(scores);\r
 340                         assertEquals(3, scores.size());\r
 341 \r
 342                         Score score = scores.get("Foobar_dundeefriends");\r
 343                         assertNotNull(score);\r
 344                         assertEquals(0, score.getRanges().size());\r
 345                         assertEquals(568, score.getScores().size());\r
 346                         assertEquals("Long", score.getMethod());\r
 347 \r
 348                         score = scores.get("Foobar");\r
 349                         assertNotNull(score);\r
 350                         assertEquals(0, score.getRanges().size());\r
 351                         assertEquals(481, score.getScores().size());\r
 352                         assertEquals("Long", score.getMethod());\r
 353 \r
 354                         score = scores.get("dundeefriends");\r
 355                         assertNotNull(score);\r
 356                         assertEquals(0, score.getRanges().size());\r
 357                         assertEquals(513, score.getScores().size());\r
 358                         assertEquals("Long", score.getMethod());\r
 359                 } catch (IOException e) {\r
 360                         e.printStackTrace();\r
 361                         fail(e.getLocalizedMessage());\r
 362                 } catch (UnknownFileFormatException e) {\r
 363                         e.printStackTrace();\r
 364                         fail(e.getLocalizedMessage());\r
 365                 }\r
 366         }\r
 367 \r
 368         @Test\r
 369         public void ReadIUPredForGlobDomain() {\r
 370                 try {\r
 371                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
 372                         assertNotNull(scores);\r
 373                         assertEquals(2, scores.size());\r
 374                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 375                         assertEquals(2, man.getNumberOfSeq());\r
 376                         Score score = scores.get("P53_HUMA");\r
 377                         assertNotNull(score);\r
 378                         assertEquals(2, score.getRanges().size());\r
 379                         assertEquals(0, score.getScores().size());\r
 380                         assertEquals("Glob", score.getMethod());\r
 381                         score = scores.get("Foobar_dundeefriends");\r
 382                         assertEquals(0, score.getRanges().size());\r
 383                 } catch (IOException e) {\r
 384                         e.printStackTrace();\r
 385                         fail(e.getLocalizedMessage());\r
 386                 } catch (UnknownFileFormatException e) {\r
 387                         e.printStackTrace();\r
 388                         fail(e.getLocalizedMessage());\r
 389                 }\r
 390         }\r
 391 \r
 392         @Test\r
 393         public void ReadAAConResults() {\r
 394                 try {\r
 395                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 396                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 397                         inStream.close();\r
 398                         assertNotNull(result);\r
 399                         assertEquals(result.size(), 18);\r
 400 \r
 401                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_result_single.out");\r
 402                         result = SequenceUtil.readAAConResults(inStream);\r
 403                         inStream.close();\r
 404                         assertNotNull(result);\r
 405                         assertEquals(result.size(), 1);\r
 406                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 407                 } catch (IOException e) {\r
 408                         e.printStackTrace();\r
 409                         fail(e.getMessage());\r
 410                 }\r
 411         }\r
 412         @Test\r
 413         public void ReadJpredResults() {\r
 414                 try {\r
 415                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");\r
 416                         List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);\r
 417                         inStream.close();\r
 418                         assertNotNull(result);\r
 419                         assertEquals(result.size(), 19);\r
 420                 } catch (IOException e) {\r
 421                         e.printStackTrace();\r
 422                         fail(e.getMessage());\r
 423                 }\r
 424         }\r
 425 }\r
 426 \r