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         // This method tests the loading of horizontally formatted Jronn output file\r
 137         @Test\r
 138         public void LoadJronnFile() {\r
 139 \r
 140                 FileInputStream fio;\r
 141                 try {\r
 142                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 143                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 144                         assertNotNull(aseqs);\r
 145                         assertEquals(aseqs.size(), 3);\r
 146                         Score aseq = aseqs.get("Foobar");\r
 147                         assertNotNull(aseq);\r
 148                         assertNotNull(aseq.getScores());\r
 149                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 150                         fio.close();\r
 151                 } catch (FileNotFoundException e) {\r
 152                         e.printStackTrace();\r
 153                         fail(e.getLocalizedMessage());\r
 154                 } catch (IOException e) {\r
 155                         e.printStackTrace();\r
 156                         fail(e.getLocalizedMessage());\r
 157                 } catch (UnknownFileFormatException e) {\r
 158                         e.printStackTrace();\r
 159                         fail(e.getLocalizedMessage());\r
 160                 }\r
 161         }\r
 162 \r
 163         enum Trial {\r
 164                 one, two, three\r
 165         };\r
 166 \r
 167         /**\r
 168          * This test tests the loading of horizontally formatted Jronn output file\r
 169          * \r
 170          * First seq\r
 171          * \r
 172          * M 0.86010 0.88512 0.37094\r
 173          * \r
 174          * T 0.79983 0.85864 0.44331\r
 175          * \r
 176          */\r
 177         @SuppressWarnings("unchecked")\r
 178         @Test\r
 179         public void ReadDisemblResults() {\r
 180                 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
 181                 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
 182                 Map<String,Map<String, Float>>  _values=new HashMap<String, Map<String,Float>>();\r
 183                 Map<String, Float> values = new HashMap<String, Float>();\r
 184                 Set<Range> rset;\r
 185                 rset = new HashSet<Range>();\r
 186                 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
 187                         rset.add(new Range(se));\r
 188                 }\r
 189                 ranges.put(DisemblResult.COILS.toString(), rset);\r
 190                 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
 191                 rset = new HashSet<Range>();\r
 192                 for (String[] se:new String[][] { { "355","368"}}) {\r
 193                         rset.add(new Range(se));\r
 194                 }\r
 195                 ranges.put(DisemblResult.REM465.toString(), rset);\r
 196                 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
 197                 rset = new HashSet<Range>();\r
 198                 for (String[] se:new String[][] { { "190","204"}}) {\r
 199                         rset.add(new Range(se));\r
 200                 }\r
 201                 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
 202                 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
 203                 _ranges.put("Foobar_dundeefriends", ranges);\r
 204                 _values.put("Foobar_dundeefriends", values);\r
 205                 FileInputStream fio;\r
 206                 try {\r
 207                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "disembl.out");\r
 208                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 209                         assertNotNull(aseqs);\r
 210                         assertEquals(aseqs.size(), 3);\r
 211                         ScoreManager sman = ScoreManager.newInstance(aseqs);\r
 212 \r
 213                         for (String fs : aseqs.keySet()) {\r
 214                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs));\r
 215                                 Set<Score> scores = aseqs.get(fs);\r
 216                                 assertEquals(scores.size(), 3);\r
 217                                 for (Score sc:scores) {\r
 218                                         if (_ranges.containsKey(fs)) {\r
 219                                                 assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
 220                                                 assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
 221                                         }\r
 222                                 }\r
 223                         }\r
 224                         fio.close();\r
 225                 } catch (FileNotFoundException e) {\r
 226                         e.printStackTrace();\r
 227                         fail(e.getLocalizedMessage());\r
 228                 } catch (IOException e) {\r
 229                         e.printStackTrace();\r
 230                         fail(e.getLocalizedMessage());\r
 231                 } catch (UnknownFileFormatException e) {\r
 232                         e.printStackTrace();\r
 233                         fail(e.getLocalizedMessage());\r
 234                 }\r
 235         }\r
 236 \r
 237         /**\r
 238          * This method tests the loading of horizontally formatted Jronn output file\r
 239          * \r
 240          * First sequence:\r
 241          * \r
 242          * >Foobar_dundeefriends\r
 243          * \r
 244          * # GlobDoms 2-358, 373-568\r
 245          * \r
 246          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 247          * \r
 248          * # RESIDUE DYDX RAW SMOOTHED\r
 249          * \r
 250          * M 0.0044 -0.2259 -0.2259\r
 251          * \r
 252          * T -0.1308 -0.2170 -0.2170\r
 253          * \r
 254          * ............\r
 255          * \r
 256          * > Second sequence\r
 257          */\r
 258         @SuppressWarnings("unchecked")\r
 259         @Test\r
 260         public void ReadGlobPlotResults() {\r
 261 \r
 262                 FileInputStream fio;\r
 263                 try {\r
 264                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "globplot.out");\r
 265                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 266                         assertNotNull(aseqs);\r
 267                         assertEquals(aseqs.size(), 3);\r
 268 \r
 269                         String fsdf = null;\r
 270                         Set<Score> scores = null;\r
 271                         for (String fs : aseqs.keySet()) {\r
 272                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 273                                         fsdf = fs;\r
 274                                         scores = aseqs.get(fs);\r
 275                                 }\r
 276                                 assertEquals(scores.size(), 5);\r
 277                         }\r
 278 \r
 279                         ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
 280                         sm.writeOut(new PrintWriter(System.out, true));\r
 281 \r
 282                         for (Score score : scores) {\r
 283                                 if (score.getMethod().equals(GlobProtResult.Disorder.toString())) {\r
 284                                         assertEquals(score.getRanges().size(), 7);\r
 285                                         assertTrue(score.getScores().isEmpty());\r
 286                                 }\r
 287                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 288                                         assertFalse(score.getScores().isEmpty());\r
 289                                         assertTrue(score.getRanges().isEmpty());\r
 290                                 }\r
 291                         }\r
 292                         fio.close();\r
 293                 } catch (FileNotFoundException e) {\r
 294                         e.printStackTrace();\r
 295                         fail(e.getLocalizedMessage());\r
 296                 } catch (IOException e) {\r
 297                         e.printStackTrace();\r
 298                         fail(e.getLocalizedMessage());\r
 299                 } catch (UnknownFileFormatException e) {\r
 300                         e.printStackTrace();\r
 301                         fail(e.getLocalizedMessage());\r
 302                 }\r
 303         }\r
 304 \r
 305         @Test\r
 306         public void ReadIUPredForShortAndLongDisorder() {\r
 307                 try {\r
 308                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "out.long"));\r
 309                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 310                         assertNotNull(scores);\r
 311                         assertEquals(3, scores.size());\r
 312 \r
 313                         Score score = scores.get("Foobar_dundeefriends");\r
 314                         assertNotNull(score);\r
 315                         assertEquals(0, score.getRanges().size());\r
 316                         assertEquals(568, score.getScores().size());\r
 317                         assertEquals("Long", score.getMethod());\r
 318 \r
 319                         score = scores.get("Foobar");\r
 320                         assertNotNull(score);\r
 321                         assertEquals(0, score.getRanges().size());\r
 322                         assertEquals(481, score.getScores().size());\r
 323                         assertEquals("Long", score.getMethod());\r
 324 \r
 325                         score = scores.get("dundeefriends");\r
 326                         assertNotNull(score);\r
 327                         assertEquals(0, score.getRanges().size());\r
 328                         assertEquals(513, score.getScores().size());\r
 329                         assertEquals("Long", score.getMethod());\r
 330                 } catch (IOException e) {\r
 331                         e.printStackTrace();\r
 332                         fail(e.getLocalizedMessage());\r
 333                 } catch (UnknownFileFormatException e) {\r
 334                         e.printStackTrace();\r
 335                         fail(e.getLocalizedMessage());\r
 336                 }\r
 337         }\r
 338 \r
 339         @Test\r
 340         public void ReadIUPredForGlobDomain() {\r
 341                 try {\r
 342                         Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
 343                         assertNotNull(scores);\r
 344                         assertEquals(2, scores.size());\r
 345                         ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
 346                         assertEquals(2, man.getNumberOfSeq());\r
 347                         Score score = scores.get("P53_HUMA");\r
 348                         assertNotNull(score);\r
 349                         assertEquals(2, score.getRanges().size());\r
 350                         assertEquals(0, score.getScores().size());\r
 351                         assertEquals("Glob", score.getMethod());\r
 352                         score = scores.get("Foobar_dundeefriends");\r
 353                         assertEquals(0, score.getRanges().size());\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
 360                 }\r
 361         }\r
 362 \r
 363         @Test\r
 364         public void ReadAAConResults() {\r
 365                 try {\r
 366                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 367                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 368                         inStream.close();\r
 369                         assertNotNull(result);\r
 370                         assertEquals(result.size(), 18);\r
 371 \r
 372                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_result_single.out");\r
 373                         result = SequenceUtil.readAAConResults(inStream);\r
 374                         inStream.close();\r
 375                         assertNotNull(result);\r
 376                         assertEquals(result.size(), 1);\r
 377                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 378                 } catch (IOException e) {\r
 379                         e.printStackTrace();\r
 380                         fail(e.getMessage());\r
 381                 }\r
 382         }\r
 383         @Test\r
 384         public void ReadJpredResults() {\r
 385                 try {\r
 386                         InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");\r
 387                         List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);\r
 388                         inStream.close();\r
 389                         assertNotNull(result);\r
 390                         assertEquals(result.size(), 19);\r
 391                 } catch (IOException e) {\r
 392                         e.printStackTrace();\r
 393                         fail(e.getMessage());\r
 394                 }\r
 395         }\r
 396 }\r