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.util.HashMap;\r
  28 import java.util.HashSet;\r
  29 import java.util.List;\r
  30 import java.util.Map;\r
  31 import java.util.Set;\r
  32 \r
  33 import org.testng.annotations.Test;\r
  34 \r
  35 import compbio.metadata.AllTestSuit;\r
  36 \r
  37 public class SequenceUtilTester {\r
  38 \r
  39         @Test()\r
  40         public void testisNonAmbNucleotideSequence() {\r
  41                 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
  42                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
  43                 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
  44                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
  45                 String nonDna = "atgfctgatgcatgcatgatgctga";\r
  46                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  47 \r
  48                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  49                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  50 \r
  51                 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  52                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  53                 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
  54                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  55 \r
  56         }\r
  57 \r
  58         @Test()\r
  59         public void testCleanSequence() {\r
  60                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  61                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  62                                 SequenceUtil.cleanSequence(dirtySeq));\r
  63         }\r
  64 \r
  65         @Test()\r
  66         public void testDeepCleanSequence() {\r
  67                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  68                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  69                                 SequenceUtil.deepCleanSequence(dirtySeq));\r
  70         }\r
  71 \r
  72         @Test()\r
  73         public void testisProteinSequence() {\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 testCleanProteinSequence() {\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\r
  92                                 .cleanProteinSequence(dirtySeq)));\r
  93 \r
  94                 String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
  95                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  96                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
  97                                 .cleanProteinSequence(notaSeq)));\r
  98 \r
  99                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
 100                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
 101                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 102                                 .cleanProteinSequence(AAseq)));\r
 103                 AAseq += "XU";\r
 104 \r
 105                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
 106                 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil\r
 107                                 .cleanProteinSequence(AAseq)));\r
 108         }\r
 109 \r
 110         @Test()\r
 111         public void testReadWriteFasta() {\r
 112 \r
 113                 try {\r
 114                         FileInputStream fio = new FileInputStream(\r
 115                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
 116                         assertNotNull(fio);\r
 117                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
 118                         assertNotNull(fseqs);\r
 119                         assertEquals(3, fseqs.size());\r
 120                         assertEquals(3, fseqs.size());\r
 121                         fio.close();\r
 122                         FileOutputStream fou = new FileOutputStream(\r
 123                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
 124                         SequenceUtil.writeFasta(fou, fseqs);\r
 125                         fou.close();\r
 126                         FileOutputStream fou20 = new FileOutputStream(\r
 127                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 128                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 129                         fou20.close();\r
 130 \r
 131                 } catch (FileNotFoundException e) {\r
 132                         e.printStackTrace();\r
 133                         fail(e.getLocalizedMessage());\r
 134                 } catch (IOException e) {\r
 135                         e.printStackTrace();\r
 136                         fail(e.getLocalizedMessage());\r
 137                 }\r
 138         }\r
 139 \r
 140         /**\r
 141          * This test tests the loading of horizontally formatted Jronn output file\r
 142          */\r
 143         @Test\r
 144         public void loadJronnFile() {\r
 145 \r
 146                 FileInputStream fio;\r
 147                 try {\r
 148                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 149                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 150                         assertNotNull(aseqs);\r
 151                         assertEquals(aseqs.size(), 3);\r
 152                         Score aseq = aseqs.get("Foobar");\r
 153                         assertNotNull(aseq);\r
 154                         assertNotNull(aseq.getScores());\r
 155                         // System.out.println(aseq);\r
 156                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 157                         fio.close();\r
 158                 } catch (FileNotFoundException e) {\r
 159                         e.printStackTrace();\r
 160                         fail(e.getLocalizedMessage());\r
 161                 } catch (IOException e) {\r
 162                         e.printStackTrace();\r
 163                         fail(e.getLocalizedMessage());\r
 164                 } catch (UnknownFileFormatException e) {\r
 165                         e.printStackTrace();\r
 166                         fail(e.getLocalizedMessage());\r
 167                 }\r
 168 \r
 169         }\r
 170 \r
 171         enum Trial {\r
 172                 one, two, three\r
 173         };\r
 174 \r
 175         /**\r
 176          * This test tests the loading of horizontally formatted Jronn output file\r
 177          * \r
 178          * First seq\r
 179          * \r
 180          * M 0.86010 0.88512 0.37094\r
 181          * \r
 182          * T 0.79983 0.85864 0.44331\r
 183          * \r
 184          */\r
 185         @SuppressWarnings("unchecked")\r
 186         @Test\r
 187         public void testReadDisemblResults() {\r
 188 \r
 189                 FileInputStream fio;\r
 190                 try {\r
 191                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 192                                         + "disembl.out");\r
 193                         Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
 194                         assertNotNull(aseqs);\r
 195                         assertEquals(aseqs.size(), 3);\r
 196                         // System.out.println(aseqs);\r
 197                         for (String fs : aseqs.keySet()) {\r
 198                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
 199                                                 .contains(fs));\r
 200                                 Set<Score> scores = aseqs.get(fs);\r
 201                                 assertEquals(scores.size(), 3);\r
 202                         }\r
 203                         fio.close();\r
 204                 } catch (FileNotFoundException e) {\r
 205                         e.printStackTrace();\r
 206                         fail(e.getLocalizedMessage());\r
 207                 } catch (IOException e) {\r
 208                         e.printStackTrace();\r
 209                         fail(e.getLocalizedMessage());\r
 210                 } catch (UnknownFileFormatException e) {\r
 211                         e.printStackTrace();\r
 212                         fail(e.getLocalizedMessage());\r
 213                 }\r
 214         }\r
 215 \r
 216         /**\r
 217          * This test tests the loading of horizontally formatted Jronn output file\r
 218          * \r
 219          * First sequence:\r
 220          * \r
 221          * >Foobar_dundeefriends\r
 222          * \r
 223          * # GlobDoms 2-358, 373-568\r
 224          * \r
 225          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 226          * \r
 227          * # RESIDUE DYDX RAW SMOOTHED\r
 228          * \r
 229          * M 0.0044 -0.2259 -0.2259\r
 230          * \r
 231          * T -0.1308 -0.2170 -0.2170\r
 232          * \r
 233          * ............\r
 234          * \r
 235          * > Second sequence\r
 236          */\r
 237         @SuppressWarnings("unchecked")\r
 238         @Test\r
 239         public void testReadGlobPlotResults() {\r
 240 \r
 241                 FileInputStream fio;\r
 242                 try {\r
 243                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 244                                         + "globplot.out");\r
 245                         HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
 246                         assertNotNull(aseqs);\r
 247                         assertEquals(aseqs.size(), 3);\r
 248 \r
 249                         String fsdf = null;\r
 250                         Set<Score> scores = null;\r
 251                         for (String fs : aseqs.keySet()) {\r
 252                                 if ("Foobar_dundeefriends".contains(fs)) {\r
 253                                         fsdf = fs;\r
 254                                         scores = aseqs.get(fs);\r
 255                                 }\r
 256                                 assertEquals(scores.size(), 5);\r
 257                         }\r
 258                         for (Score score : scores) {\r
 259 \r
 260                                 if (score.getMethod()\r
 261                                                 .equals(GlobProtResult.Disorder.toString())) {\r
 262                                         assertEquals(score.getRanges().size(), 7);\r
 263                                         assertTrue(score.getScores().isEmpty());\r
 264                                 }\r
 265                                 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
 266                                         assertFalse(score.getScores().isEmpty());\r
 267                                         assertTrue(score.getRanges().isEmpty());\r
 268                                 }\r
 269                         }\r
 270                         fio.close();\r
 271                 } catch (FileNotFoundException e) {\r
 272                         e.printStackTrace();\r
 273                         fail(e.getLocalizedMessage());\r
 274                 } catch (IOException e) {\r
 275                         e.printStackTrace();\r
 276                         fail(e.getLocalizedMessage());\r
 277                 } catch (UnknownFileFormatException e) {\r
 278                         e.printStackTrace();\r
 279                         fail(e.getLocalizedMessage());\r
 280                 }\r
 281         }\r
 282 \r
 283         @Test\r
 284         public void testReadAAConResults() {\r
 285                 try {\r
 286                         InputStream inStream = new FileInputStream(\r
 287                                         AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 288                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 289                         inStream.close();\r
 290                         assertNotNull(result);\r
 291                         assertEquals(result.size(), 18);\r
 292 \r
 293                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 294                                         + "aacon_result_single.out");\r
 295                         result = SequenceUtil.readAAConResults(inStream);\r
 296                         inStream.close();\r
 297                         assertNotNull(result);\r
 298                         assertEquals(result.size(), 1);\r
 299                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 300                 } catch (IOException e) {\r
 301                         e.printStackTrace();\r
 302                         fail(e.getMessage());\r
 303                 }\r
 304         }\r
 305 }\r