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 \r
  39 public class SequenceUtilTester {\r
  40 \r
  41         @Test()\r
  42         public void testisNonAmbNucleotideSequence() {\r
  43                 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
  44                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
  45                 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
  46                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
  47                 String nonDna = "atgfctgatgcatgcatgatgctga";\r
  48                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  49 \r
  50                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  51                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  52 \r
  53                 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  54                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  55                 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
  56                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  57 \r
  58         }\r
  59 \r
  60         @Test()\r
  61         public void testCleanSequence() {\r
  62                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  63                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  64                                 SequenceUtil.cleanSequence(dirtySeq));\r
  65         }\r
  66 \r
  67         @Test()\r
  68         public void testDeepCleanSequence() {\r
  69                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  70                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  71                                 SequenceUtil.deepCleanSequence(dirtySeq));\r
  72         }\r
  73 \r
  74         @Test()\r
  75         public void testisProteinSequence() {\r
  76                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  77                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  78                 String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
  79                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  80                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  81                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  82                 AAseq += "XU";\r
  83                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  84 \r
  85         }\r
  86 \r
  87         @Test()\r
  88         public void testCleanProteinSequence() {\r
  89                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  90                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  91                 // This will still be NON protein sequence despite having only correct\r
  92                 // letters because the letters match perfectly the nucleotide sequence!\r
  93                 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil\r
  94                                 .cleanProteinSequence(dirtySeq)));\r
  95 \r
  96                 String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
  97                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  98                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
  99                                 .cleanProteinSequence(notaSeq)));\r
 100 \r
 101                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
 102                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
 103                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 104                                 .cleanProteinSequence(AAseq)));\r
 105                 AAseq += "XU";\r
 106 \r
 107                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
 108                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 109                                 .cleanProteinSequence(AAseq)));\r
 110         }\r
 111 \r
 112         @Test()\r
 113         public void testReadWriteFasta() {\r
 114 \r
 115                 try {\r
 116                         FileInputStream fio = new FileInputStream(\r
 117                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 118                         assertNotNull(fio);\r
 119                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 120                         assertNotNull(fseqs);\r
 121                         assertEquals(3, fseqs.size());\r
 122                         assertEquals(3, fseqs.size());\r
 123                         fio.close();\r
 124                         FileOutputStream fou = new FileOutputStream(\r
 125                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
 126                         SequenceUtil.writeFasta(fou, fseqs);\r
 127                         fou.close();\r
 128                         FileOutputStream fou20 = new FileOutputStream(\r
 129                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 130                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 131                         fou20.close();\r
 132 \r
 133                 } catch (FileNotFoundException e) {\r
 134                         e.printStackTrace();\r
 135                         fail(e.getLocalizedMessage());\r
 136                 } catch (IOException e) {\r
 137                         e.printStackTrace();\r
 138                         fail(e.getLocalizedMessage());\r
 139                 }\r
 140         }\r
 141 \r
 142         /**\r
 143          * This test tests the loading of horizontally formatted Jronn output file\r
 144          */\r
 145         @Test\r
 146         public void loadJronnFile() {\r
 147 \r
 148                 FileInputStream fio;\r
 149                 try {\r
 150                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 151                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 152                         assertNotNull(aseqs);\r
 153                         assertEquals(aseqs.size(), 3);\r
 154                         Score aseq = aseqs.get("Foobar");\r
 155                         assertNotNull(aseq);\r
 156                         assertNotNull(aseq.getScores());\r
 157                         // System.out.println(aseq);\r
 158                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 159                         fio.close();\r
 160                 } catch (FileNotFoundException e) {\r
 161                         e.printStackTrace();\r
 162                         fail(e.getLocalizedMessage());\r
 163                 } catch (IOException e) {\r
 164                         e.printStackTrace();\r
 165                         fail(e.getLocalizedMessage());\r
 166                 } catch (UnknownFileFormatException e) {\r
 167                         e.printStackTrace();\r
 168                         fail(e.getLocalizedMessage());\r
 169                 }\r
 170 \r
 171         }\r
 172 \r
 173         enum Trial {\r
 174                 one, two, three\r
 175         };\r
 176 \r
 177         /**\r
 178          * This test tests the loading of horizontally formatted Jronn output file\r
 179          * \r
 180          * First seq\r
 181          * \r
 182          * M 0.86010 0.88512 0.37094\r
 183          * \r
 184          * T 0.79983 0.85864 0.44331\r
 185          * \r
 186          */\r
 187         @SuppressWarnings("unchecked")\r
 188         @Test\r
 189         public void testReadDisemblResults() {\r
 190 \r
 191                 FileInputStream fio;\r
 192                 try {\r
 193                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 194                                         + "disembl.out");\r
 195                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 196                         assertNotNull(aseqs);\r
 197                         assertEquals(aseqs.size(), 3);\r
 198                         ScoreManager sman = ScoreManager.newInstance(aseqs);\r
 199 \r
 200                         for (String fs : aseqs.keySet()) {\r
 201                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
 202                                                 .contains(fs));\r
 203                                 Set<Score> scores = aseqs.get(fs);\r
 204                                 assertEquals(scores.size(), 3);\r
 205                         }\r
 206                         fio.close();\r
 207                 } catch (FileNotFoundException e) {\r
 208                         e.printStackTrace();\r
 209                         fail(e.getLocalizedMessage());\r
 210                 } catch (IOException e) {\r
 211                         e.printStackTrace();\r
 212                         fail(e.getLocalizedMessage());\r
 213                 } catch (UnknownFileFormatException e) {\r
 214                         e.printStackTrace();\r
 215                         fail(e.getLocalizedMessage());\r
 216                 }\r
 217         }\r
 218 \r
 219         /**\r
 220          * This test tests the loading of horizontally formatted Jronn output file\r
 221          * \r
 222          * First sequence:\r
 223          * \r
 224          * >Foobar_dundeefriends\r
 225          * \r
 226          * # GlobDoms 2-358, 373-568\r
 227          * \r
 228          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 229          * \r
 230          * # RESIDUE DYDX RAW SMOOTHED\r
 231          * \r
 232          * M 0.0044 -0.2259 -0.2259\r
 233          * \r
 234          * T -0.1308 -0.2170 -0.2170\r
 235          * \r
 236          * ............\r
 237          * \r
 238          * > Second sequence\r
 239          */\r
 240         @SuppressWarnings("unchecked")\r
 241         @Test\r
 242         public void testReadGlobPlotResults() {\r
 243 \r
 244                 FileInputStream fio;\r
 245                 try {\r
 246                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 247                                         + "globplot.out");\r
 248                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 249                         assertNotNull(aseqs);\r
 250                         assertEquals(aseqs.size(), 3);\r
 251 \r
 252                         String fsdf = null;\r
 253                         Set<Score> scores = null;\r
 254                         for (String fs : aseqs.keySet()) {\r
 255                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 256                                         fsdf = fs;\r
 257                                         scores = aseqs.get(fs);\r
 258                                 }\r
 259                                 assertEquals(scores.size(), 5);\r
 260                         }\r
 261 \r
 262                         ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
 263                         sm.writeOut(new PrintWriter(System.out, true));\r
 264 \r
 265                         for (Score score : scores) {\r
 266 \r
 267                                 if (score.getMethod()\r
 268                                                 .equals(GlobProtResult.Disorder.toString())) {\r
 269                                         assertEquals(score.getRanges().size(), 7);\r
 270                                         assertTrue(score.getScores().isEmpty());\r
 271                                 }\r
 272                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 273                                         assertFalse(score.getScores().isEmpty());\r
 274                                         assertTrue(score.getRanges().isEmpty());\r
 275                                 }\r
 276                         }\r
 277                         fio.close();\r
 278                 } catch (FileNotFoundException e) {\r
 279                         e.printStackTrace();\r
 280                         fail(e.getLocalizedMessage());\r
 281                 } catch (IOException e) {\r
 282                         e.printStackTrace();\r
 283                         fail(e.getLocalizedMessage());\r
 284                 } catch (UnknownFileFormatException e) {\r
 285                         e.printStackTrace();\r
 286                         fail(e.getLocalizedMessage());\r
 287                 }\r
 288         }\r
 289 \r
 290         @Test\r
 291         public void testReadIUPredForShortAndLongDisorder() {\r
 292                 try {\r
 293                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
 294                                         AllTestSuit.TEST_DATA_PATH, "out.long"));\r
 295                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 296                         // man.writeOut(new PrintWriter(System.out, true));\r
 297                         assertNotNull(scores);\r
 298                         assertEquals(3, scores.size());\r
 299 \r
 300                         Score score = scores.get("Foobar_dundeefriends");\r
 301                         assertNotNull(score);\r
 302                         assertEquals(0, score.getRanges().size());\r
 303                         assertEquals(568, score.getScores().size());\r
 304                         assertEquals("Long", score.getMethod());\r
 305                         \r
 306                         score = scores.get("Foobar");\r
 307                         assertNotNull(score);\r
 308                         assertEquals(0, score.getRanges().size());\r
 309                         assertEquals(481, score.getScores().size());\r
 310                         assertEquals("Long", score.getMethod());\r
 311                         \r
 312                         score = scores.get("dundeefriends");\r
 313                         assertNotNull(score);\r
 314                         assertEquals(0, score.getRanges().size());\r
 315                         assertEquals(513, score.getScores().size());\r
 316                         assertEquals("Long", score.getMethod());\r
 317                         \r
 318                 } catch (IOException e) {\r
 319                         e.printStackTrace();\r
 320                         fail(e.getLocalizedMessage());\r
 321                 } catch (UnknownFileFormatException e) {\r
 322                         e.printStackTrace();\r
 323                         fail(e.getLocalizedMessage());\r
 324                 }\r
 325         }\r
 326 \r
 327         @Test\r
 328         public void testReadIUPredForGlobDomain() {\r
 329                 try {\r
 330                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(\r
 331                                         AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
 332                         assertNotNull(scores);\r
 333                         assertEquals(2, scores.size());\r
 334                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 335                         // man.writeOut(new PrintWriter(System.out, true));\r
 336                         assertEquals(2, man.getNumberOfSeq());\r
 337                         Score score = scores.get("P53_HUMA");\r
 338                         assertNotNull(score);\r
 339                         assertEquals(2, score.getRanges().size());\r
 340                         assertEquals(0, score.getScores().size());\r
 341                         assertEquals("Glob", score.getMethod());\r
 342 \r
 343                         score = scores.get("Foobar_dundeefriends");\r
 344                         assertEquals(0, score.getRanges().size());\r
 345                 } catch (IOException e) {\r
 346                         e.printStackTrace();\r
 347                         fail(e.getLocalizedMessage());\r
 348                 } catch (UnknownFileFormatException e) {\r
 349                         e.printStackTrace();\r
 350                         fail(e.getLocalizedMessage());\r
 351                 }\r
 352         }\r
 353         @Test\r
 354         public void testReadAAConResults() {\r
 355                 try {\r
 356                         InputStream inStream = new FileInputStream(\r
 357                                         AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 358                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 359                         inStream.close();\r
 360                         assertNotNull(result);\r
 361                         assertEquals(result.size(), 18);\r
 362 \r
 363                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 364                                         + "aacon_result_single.out");\r
 365                         result = SequenceUtil.readAAConResults(inStream);\r
 366                         inStream.close();\r
 367                         assertNotNull(result);\r
 368                         assertEquals(result.size(), 1);\r
 369                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 370                 } catch (IOException e) {\r
 371                         e.printStackTrace();\r
 372                         fail(e.getMessage());\r
 373                 }\r
 374         }\r
 375 }\r