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 isNonAmbNucleotideSequence() {\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         @Test()\r
  61         public void CleanSequence() {\r
  62                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  63                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.cleanSequence(dirtySeq));\r
  64         }\r
  65 \r
  66         @Test()\r
  67         public void DeepCleanSequence() {\r
  68                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  69                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.deepCleanSequence(dirtySeq));\r
  70         }\r
  71 \r
  72         @Test()\r
  73         public void isProteinSequence() {\r
  74                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  75                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  76                 String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
  77                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  78                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  79                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  80                 AAseq += "XU";\r
  81                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  82 \r
  83         }\r
  84 \r
  85         @Test()\r
  86         public void CleanProteinSequence() {\r
  87                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  88                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  89                 // This will still be NON protein sequence despite having only correct\r
  90                 // letters because the letters match perfectly the nucleotide sequence!\r
  91                 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(dirtySeq)));\r
  92 \r
  93                 String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
  94                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  95                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(notaSeq)));\r
  96 \r
  97                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  98                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  99                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
 100                 AAseq += "XU";\r
 101 \r
 102                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
 103                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
 104         }\r
 105 \r
 106         @Test()\r
 107         public void ReadWriteFasta() {\r
 108                 try {\r
 109                         FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 110                         assertNotNull(fio);\r
 111                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 112                         assertNotNull(fseqs);\r
 113                         assertEquals(3, fseqs.size());\r
 114                         assertEquals(3, fseqs.size());\r
 115                         fio.close();\r
 116                         FileOutputStream fou = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
 117                         SequenceUtil.writeFasta(fou, fseqs);\r
 118                         fou.close();\r
 119                         FileOutputStream fou20 = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 120                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 121                         fou20.close();\r
 122                 } catch (FileNotFoundException e) {\r
 123                         e.printStackTrace();\r
 124                         fail(e.getLocalizedMessage());\r
 125                 } catch (IOException e) {\r
 126                         e.printStackTrace();\r
 127                         fail(e.getLocalizedMessage());\r
 128                 }\r
 129         }\r
 130 \r
 131         // This method tests the loading of horizontally formatted Jronn output file\r
 132         @Test\r
 133         public void LoadJronnFile() {\r
 134 \r
 135                 FileInputStream fio;\r
 136                 try {\r
 137                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 138                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 139                         assertNotNull(aseqs);\r
 140                         assertEquals(aseqs.size(), 3);\r
 141                         Score aseq = aseqs.get("Foobar");\r
 142                         assertNotNull(aseq);\r
 143                         assertNotNull(aseq.getScores());\r
 144                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 145                         fio.close();\r
 146                 } catch (FileNotFoundException e) {\r
 147                         e.printStackTrace();\r
 148                         fail(e.getLocalizedMessage());\r
 149                 } catch (IOException e) {\r
 150                         e.printStackTrace();\r
 151                         fail(e.getLocalizedMessage());\r
 152                 } catch (UnknownFileFormatException e) {\r
 153                         e.printStackTrace();\r
 154                         fail(e.getLocalizedMessage());\r
 155                 }\r
 156         }\r
 157 \r
 158         enum Trial {\r
 159                 one, two, three\r
 160         };\r
 161 \r
 162         /**\r
 163          * This test tests the loading of horizontally formatted Jronn output file\r
 164          * \r
 165          * First seq\r
 166          * \r
 167          * M 0.86010 0.88512 0.37094\r
 168          * \r
 169          * T 0.79983 0.85864 0.44331\r
 170          * \r
 171          */\r
 172         @SuppressWarnings("unchecked")\r
 173         @Test\r
 174         public void ReadDisemblResults() {\r
 175                 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
 176                 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
 177                 Map<String,Map<String, Float>>  _values=new HashMap<String, Map<String,Float>>();\r
 178                 Map<String, Float> values = new HashMap<String, Float>();\r
 179                 Set<Range> rset;\r
 180                 rset = new HashSet<Range>();\r
 181                 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
 182                         rset.add(new Range(se));\r
 183                 }\r
 184                 ranges.put(DisemblResult.COILS.toString(), rset);\r
 185                 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
 186                 rset = new HashSet<Range>();\r
 187                 for (String[] se:new String[][] { { "355","368"}}) {\r
 188                         rset.add(new Range(se));\r
 189                 }\r
 190                 ranges.put(DisemblResult.REM465.toString(), rset);\r
 191                 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
 192                 rset = new HashSet<Range>();\r
 193                 for (String[] se:new String[][] { { "190","204"}}) {\r
 194                         rset.add(new Range(se));\r
 195                 }\r
 196                 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
 197                 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
 198                 _ranges.put("Foobar_dundeefriends", ranges);\r
 199                 _values.put("Foobar_dundeefriends", values);\r
 200                 FileInputStream fio;\r
 201                 try {\r
 202                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "disembl.out");\r
 203                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 204                         assertNotNull(aseqs);\r
 205                         assertEquals(aseqs.size(), 3);\r
 206                         ScoreManager sman = ScoreManager.newInstance(aseqs);\r
 207 \r
 208                         for (String fs : aseqs.keySet()) {\r
 209                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs));\r
 210                                 Set<Score> scores = aseqs.get(fs);\r
 211                                 assertEquals(scores.size(), 3);\r
 212                                 for (Score sc:scores) {\r
 213                                         if (_ranges.containsKey(fs)) {\r
 214                                                 assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
 215                                                 assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
 216                                         }\r
 217                                 }\r
 218                         }\r
 219                         fio.close();\r
 220                 } catch (FileNotFoundException e) {\r
 221                         e.printStackTrace();\r
 222                         fail(e.getLocalizedMessage());\r
 223                 } catch (IOException e) {\r
 224                         e.printStackTrace();\r
 225                         fail(e.getLocalizedMessage());\r
 226                 } catch (UnknownFileFormatException e) {\r
 227                         e.printStackTrace();\r
 228                         fail(e.getLocalizedMessage());\r
 229                 }\r
 230         }\r
 231 \r
 232         /**\r
 233          * This method tests the loading of horizontally formatted Jronn output file\r
 234          * \r
 235          * First sequence:\r
 236          * \r
 237          * >Foobar_dundeefriends\r
 238          * \r
 239          * # GlobDoms 2-358, 373-568\r
 240          * \r
 241          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 242          * \r
 243          * # RESIDUE DYDX RAW SMOOTHED\r
 244          * \r
 245          * M 0.0044 -0.2259 -0.2259\r
 246          * \r
 247          * T -0.1308 -0.2170 -0.2170\r
 248          * \r
 249          * ............\r
 250          * \r
 251          * > Second sequence\r
 252          */\r
 253         @SuppressWarnings("unchecked")\r
 254         @Test\r
 255         public void ReadGlobPlotResults() {\r
 256 \r
 257                 FileInputStream fio;\r
 258                 try {\r
 259                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "globplot.out");\r
 260                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 261                         assertNotNull(aseqs);\r
 262                         assertEquals(aseqs.size(), 3);\r
 263 \r
 264                         String fsdf = null;\r
 265                         Set<Score> scores = null;\r
 266                         for (String fs : aseqs.keySet()) {\r
 267                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 268                                         fsdf = fs;\r
 269                                         scores = aseqs.get(fs);\r
 270                                 }\r
 271                                 assertEquals(scores.size(), 5);\r
 272                         }\r
 273 \r
 274                         ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
 275                         sm.writeOut(new PrintWriter(System.out, true));\r
 276 \r
 277                         for (Score score : scores) {\r
 278                                 if (score.getMethod().equals(GlobProtResult.Disorder.toString())) {\r
 279                                         assertEquals(score.getRanges().size(), 7);\r
 280                                         assertTrue(score.getScores().isEmpty());\r
 281                                 }\r
 282                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 283                                         assertFalse(score.getScores().isEmpty());\r
 284                                         assertTrue(score.getRanges().isEmpty());\r
 285                                 }\r
 286                         }\r
 287                         fio.close();\r
 288                 } catch (FileNotFoundException e) {\r
 289                         e.printStackTrace();\r
 290                         fail(e.getLocalizedMessage());\r
 291                 } catch (IOException e) {\r
 292                         e.printStackTrace();\r
 293                         fail(e.getLocalizedMessage());\r
 294                 } catch (UnknownFileFormatException e) {\r
 295                         e.printStackTrace();\r
 296                         fail(e.getLocalizedMessage());\r
 297                 }\r
 298         }\r
 299 \r
 300         @Test\r
 301         public void ReadIUPredForShortAndLongDisorder() {\r
 302                 try {\r
 303                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "out.long"));\r
 304                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 305                         assertNotNull(scores);\r
 306                         assertEquals(3, scores.size());\r
 307 \r
 308                         Score score = scores.get("Foobar_dundeefriends");\r
 309                         assertNotNull(score);\r
 310                         assertEquals(0, score.getRanges().size());\r
 311                         assertEquals(568, score.getScores().size());\r
 312                         assertEquals("Long", score.getMethod());\r
 313 \r
 314                         score = scores.get("Foobar");\r
 315                         assertNotNull(score);\r
 316                         assertEquals(0, score.getRanges().size());\r
 317                         assertEquals(481, score.getScores().size());\r
 318                         assertEquals("Long", score.getMethod());\r
 319 \r
 320                         score = scores.get("dundeefriends");\r
 321                         assertNotNull(score);\r
 322                         assertEquals(0, score.getRanges().size());\r
 323                         assertEquals(513, score.getScores().size());\r
 324                         assertEquals("Long", score.getMethod());\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 ReadIUPredForGlobDomain() {\r
 336                 try {\r
 337                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
 338                         assertNotNull(scores);\r
 339                         assertEquals(2, scores.size());\r
 340                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 341                         assertEquals(2, man.getNumberOfSeq());\r
 342                         Score score = scores.get("P53_HUMA");\r
 343                         assertNotNull(score);\r
 344                         assertEquals(2, score.getRanges().size());\r
 345                         assertEquals(0, score.getScores().size());\r
 346                         assertEquals("Glob", score.getMethod());\r
 347                         score = scores.get("Foobar_dundeefriends");\r
 348                         assertEquals(0, score.getRanges().size());\r
 349                 } catch (IOException e) {\r
 350                         e.printStackTrace();\r
 351                         fail(e.getLocalizedMessage());\r
 352                 } catch (UnknownFileFormatException e) {\r
 353                         e.printStackTrace();\r
 354                         fail(e.getLocalizedMessage());\r
 355                 }\r
 356         }\r
 357 \r
 358         @Test\r
 359         public void ReadAAConResults() {\r
 360                 try {\r
 361                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 362                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 363                         inStream.close();\r
 364                         assertNotNull(result);\r
 365                         assertEquals(result.size(), 18);\r
 366 \r
 367                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_result_single.out");\r
 368                         result = SequenceUtil.readAAConResults(inStream);\r
 369                         inStream.close();\r
 370                         assertNotNull(result);\r
 371                         assertEquals(result.size(), 1);\r
 372                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 373                 } catch (IOException e) {\r
 374                         e.printStackTrace();\r
 375                         fail(e.getMessage());\r
 376                 }\r
 377         }\r
 378         @Test\r
 379         public void ReadJpredResults() {\r
 380                 try {\r
 381                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");\r
 382                         List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);\r
 383                         inStream.close();\r
 384                         assertNotNull(result);\r
 385                         assertEquals(result.size(), 19);\r
 386                 } catch (IOException e) {\r
 387                         e.printStackTrace();\r
 388                         fail(e.getMessage());\r
 389                 }\r
 390         }\r
 391 }\r