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 testReadWriteFasta() {\r
  87 \r
  88                 try {\r
  89                         FileInputStream fio = new FileInputStream(\r
  90                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
  91                         assertNotNull(fio);\r
  92                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
  93                         assertNotNull(fseqs);\r
  94                         assertEquals(3, fseqs.size());\r
  95                         assertEquals(3, fseqs.size());\r
  96                         fio.close();\r
  97                         FileOutputStream fou = new FileOutputStream(\r
  98                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
  99                         SequenceUtil.writeFasta(fou, fseqs);\r
 100                         fou.close();\r
 101                         FileOutputStream fou20 = new FileOutputStream(\r
 102                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 103                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 104                         fou20.close();\r
 105 \r
 106                 } catch (FileNotFoundException e) {\r
 107                         e.printStackTrace();\r
 108                         fail(e.getLocalizedMessage());\r
 109                 } catch (IOException e) {\r
 110                         e.printStackTrace();\r
 111                         fail(e.getLocalizedMessage());\r
 112                 }\r
 113         }\r
 114 \r
 115         /**\r
 116          * This test tests the loading of horizontally formatted Jronn output file\r
 117          */\r
 118         @Test\r
 119         public void loadJronnFile() {\r
 120 \r
 121                 FileInputStream fio;\r
 122                 try {\r
 123                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 124                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 125                         assertNotNull(aseqs);\r
 126                         assertEquals(aseqs.size(), 3);\r
 127                         Score aseq = aseqs.get("Foobar");\r
 128                         assertNotNull(aseq);\r
 129                         assertNotNull(aseq.getScores());\r
 130                         // System.out.println(aseq);\r
 131                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 132                         fio.close();\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                 } catch (UnknownFileFormatException e) {\r
 140                         e.printStackTrace();\r
 141                         fail(e.getLocalizedMessage());\r
 142                 }\r
 143 \r
 144         }\r
 145 \r
 146         enum Trial {\r
 147                 one, two, three\r
 148         };\r
 149 \r
 150         /**\r
 151          * This test tests the loading of horizontally formatted Jronn output file\r
 152          * \r
 153          * First seq\r
 154          * \r
 155          * M 0.86010 0.88512 0.37094\r
 156          * \r
 157          * T 0.79983 0.85864 0.44331\r
 158          * \r
 159          */\r
 160         @SuppressWarnings("unchecked")\r
 161         @Test\r
 162         public void testReadDisemblResults() {\r
 163 \r
 164                 FileInputStream fio;\r
 165                 try {\r
 166                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 167                                         + "disembl.out");\r
 168                         Map<FastaSequence, HashSet<Score>> aseqs = SequenceUtil\r
 169                                         .readDisembl(fio);\r
 170                         assertNotNull(aseqs);\r
 171                         assertEquals(aseqs.size(), 3);\r
 172                         // System.out.println(aseqs);\r
 173                         for (FastaSequence fs : aseqs.keySet()) {\r
 174                                 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
 175                                                 .contains(fs.getId()));\r
 176                                 Set<Score> scores = aseqs.get(fs);\r
 177                                 assertEquals(scores.size(), 3);\r
 178                         }\r
 179                         fio.close();\r
 180                 } catch (FileNotFoundException e) {\r
 181                         e.printStackTrace();\r
 182                         fail(e.getLocalizedMessage());\r
 183                 } catch (IOException e) {\r
 184                         e.printStackTrace();\r
 185                         fail(e.getLocalizedMessage());\r
 186                 } catch (UnknownFileFormatException e) {\r
 187                         e.printStackTrace();\r
 188                         fail(e.getLocalizedMessage());\r
 189                 }\r
 190         }\r
 191 \r
 192         /**\r
 193          * This test tests the loading of horizontally formatted Jronn output file\r
 194          * \r
 195          * First sequence:\r
 196          * \r
 197          * >Foobar_dundeefriends\r
 198          * \r
 199          * # GlobDoms 2-358, 373-568\r
 200          * \r
 201          * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
 202          * \r
 203          * # RESIDUE DYDX RAW SMOOTHED\r
 204          * \r
 205          * M 0.0044 -0.2259 -0.2259\r
 206          * \r
 207          * T -0.1308 -0.2170 -0.2170\r
 208          * \r
 209          * ............\r
 210          * \r
 211          * > Second sequence\r
 212          */\r
 213         @SuppressWarnings("unchecked")\r
 214         @Test\r
 215         public void testReadGlobPlotResults() {\r
 216 \r
 217                 FileInputStream fio;\r
 218                 try {\r
 219                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 220                                         + "globplot.out");\r
 221                         HashMap<FastaSequence, HashSet<Score>> aseqs = SequenceUtil\r
 222                                         .readGlobPlot(fio);\r
 223                         assertNotNull(aseqs);\r
 224                         assertEquals(aseqs.size(), 3);\r
 225 \r
 226                         FastaSequence fsdf = null;\r
 227                         Set<Score> scores = null;\r
 228                         for (FastaSequence fs : aseqs.keySet()) {\r
 229                                 if ("Foobar_dundeefriends".contains(fs.getId())) {\r
 230                                         fsdf = fs;\r
 231                                         scores = aseqs.get(fs);\r
 232                                 }\r
 233                                 assertEquals(scores.size(), 5);\r
 234                         }\r
 235                         for (Score score : scores) {\r
 236 \r
 237                                 if (score.getMethod() == (Enum<?>) GlobProtResult.Disorder) {\r
 238                                         assertEquals(score.getRanges().size(), 7);\r
 239                                         assertTrue(score.getScores().isEmpty());\r
 240                                 }\r
 241                                 if (score.getMethod() == (Enum<?>) GlobProtResult.Dydx) {\r
 242                                         assertFalse(score.getScores().isEmpty());\r
 243                                         assertTrue(score.getRanges().isEmpty());\r
 244                                 }\r
 245                         }\r
 246                         fio.close();\r
 247                 } catch (FileNotFoundException e) {\r
 248                         e.printStackTrace();\r
 249                         fail(e.getLocalizedMessage());\r
 250                 } catch (IOException e) {\r
 251                         e.printStackTrace();\r
 252                         fail(e.getLocalizedMessage());\r
 253                 } catch (UnknownFileFormatException e) {\r
 254                         e.printStackTrace();\r
 255                         fail(e.getLocalizedMessage());\r
 256                 }\r
 257         }\r
 258 \r
 259         @Test\r
 260         public void testReadAAConResults() {\r
 261                 try {\r
 262                         InputStream inStream = new FileInputStream(\r
 263                                         AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 264                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 265                         inStream.close();\r
 266                         assertNotNull(result);\r
 267                         assertEquals(result.size(), 18);\r
 268 \r
 269                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 270                                         + "aacon_result_single.out");\r
 271                         result = SequenceUtil.readAAConResults(inStream);\r
 272                         inStream.close();\r
 273                         assertNotNull(result);\r
 274                         assertEquals(result.size(), 1);\r
 275                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 276                 } catch (IOException e) {\r
 277                         e.printStackTrace();\r
 278                         fail(e.getMessage());\r
 279                 }\r
 280         }\r
 281 }\r