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.HashSet;\r
  28 import java.util.List;\r
  29 import java.util.Map;\r
  30 import java.util.Set;\r
  31 \r
  32 import org.testng.annotations.Test;\r
  33 \r
  34 import compbio.metadata.AllTestSuit;\r
  35 \r
  36 public class SequenceUtilTester {\r
  37 \r
  38         @Test()\r
  39         public void testisNonAmbNucleotideSequence() {\r
  40                 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
  41                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
  42                 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
  43                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
  44                 String nonDna = "atgfctgatgcatgcatgatgctga";\r
  45                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  46 \r
  47                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  48                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  49 \r
  50                 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  51                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  52                 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
  53                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  54 \r
  55         }\r
  56 \r
  57         @Test()\r
  58         public void testCleanSequence() {\r
  59                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  60                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  61                                 SequenceUtil.cleanSequence(dirtySeq));\r
  62         }\r
  63 \r
  64         @Test()\r
  65         public void testDeepCleanSequence() {\r
  66                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  67                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  68                                 SequenceUtil.deepCleanSequence(dirtySeq));\r
  69         }\r
  70 \r
  71         @Test()\r
  72         public void testisProteinSequence() {\r
  73                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  74                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  75                 String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
  76                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  77                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  78                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  79                 AAseq += "XU";\r
  80                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  81 \r
  82         }\r
  83 \r
  84         @Test()\r
  85         public void testReadWriteFasta() {\r
  86 \r
  87                 try {\r
  88                         FileInputStream fio = new FileInputStream(\r
  89                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
  90                         assertNotNull(fio);\r
  91                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
  92                         assertNotNull(fseqs);\r
  93                         assertEquals(3, fseqs.size());\r
  94                         assertEquals(3, fseqs.size());\r
  95                         fio.close();\r
  96                         FileOutputStream fou = new FileOutputStream(\r
  97                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
  98                         SequenceUtil.writeFasta(fou, fseqs);\r
  99                         fou.close();\r
 100                         FileOutputStream fou20 = new FileOutputStream(\r
 101                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
 102                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 103                         fou20.close();\r
 104 \r
 105                 } catch (FileNotFoundException e) {\r
 106                         e.printStackTrace();\r
 107                         fail(e.getLocalizedMessage());\r
 108                 } catch (IOException e) {\r
 109                         e.printStackTrace();\r
 110                         fail(e.getLocalizedMessage());\r
 111                 }\r
 112         }\r
 113 \r
 114         /**\r
 115          * This test tests the loading of horizontally formatted Jronn output file\r
 116          */\r
 117         @Test\r
 118         public void loadJronnFile() {\r
 119 \r
 120                 FileInputStream fio;\r
 121                 try {\r
 122                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 123                         Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
 124                         assertNotNull(aseqs);\r
 125                         assertEquals(aseqs.size(), 3);\r
 126                         Score aseq = aseqs.get("Foobar");\r
 127                         assertNotNull(aseq);\r
 128                         assertNotNull(aseq.getScores());\r
 129                         // System.out.println(aseq);\r
 130                         assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
 131                         fio.close();\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                 } catch (UnknownFileFormatException e) {\r
 139                         e.printStackTrace();\r
 140                         fail(e.getLocalizedMessage());\r
 141                 }\r
 142 \r
 143         }\r
 144 \r
 145         enum Trial {\r
 146                 one, two, three\r
 147         };\r
 148 \r
 149         /**\r
 150          * This test tests the loading of horizontally formatted Jronn output file\r
 151          */\r
 152         @SuppressWarnings("unchecked")\r
 153         @Test\r
 154         public void testMultiAnnotatedSequence() {\r
 155 \r
 156                 FileInputStream fio;\r
 157                 try {\r
 158                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 159                                         + "disembl.out");\r
 160                         Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
 161                                         .readDisembl(fio);\r
 162                         assertNotNull(aseqs);\r
 163 \r
 164                         /*\r
 165                          * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);\r
 166                          * List<Number> list = new ArrayList<Number>(); list.add(new\r
 167                          * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,\r
 168                          * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));\r
 169                          * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);\r
 170                          */\r
 171                         fio.close();\r
 172                 } catch (FileNotFoundException e) {\r
 173                         e.printStackTrace();\r
 174                         fail(e.getLocalizedMessage());\r
 175                 } catch (IOException e) {\r
 176                         e.printStackTrace();\r
 177                         fail(e.getLocalizedMessage());\r
 178                 } catch (UnknownFileFormatException e) {\r
 179                         e.printStackTrace();\r
 180                         fail(e.getLocalizedMessage());\r
 181                 }\r
 182         }\r
 183 \r
 184         @Test\r
 185         public void testReadAAConResults() {\r
 186                 try {\r
 187                         InputStream inStream = new FileInputStream(\r
 188                                         AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
 189                         HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
 190                         inStream.close();\r
 191                         assertNotNull(result);\r
 192                         assertEquals(result.size(), 18);\r
 193 \r
 194                         inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 195                                         + "aacon_result_single.out");\r
 196                         result = SequenceUtil.readAAConResults(inStream);\r
 197                         inStream.close();\r
 198                         assertNotNull(result);\r
 199                         assertEquals(result.size(), 1);\r
 200                         assertEquals(result.iterator().next().getScores().size(), 568);\r
 201                 } catch (IOException e) {\r
 202                         e.printStackTrace();\r
 203                         fail(e.getMessage());\r
 204                 }\r
 205         }\r
 206 }\r