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