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