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.List;\r
  28 \r
  29 import org.testng.annotations.Test;\r
  30 \r
  31 import compbio.metadata.AllTestSuit;\r
  32 \r
  33 public class SequenceUtilTester {\r
  34 \r
  35         @Test()\r
  36         public void testisNonAmbNucleotideSequence() {\r
  37                 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
  38                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
  39                 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
  40                 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
  41                 String nonDna = "atgfctgatgcatgcatgatgctga";\r
  42                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  43 \r
  44                 nonDna = "atgc1tgatgcatgcatgatgctga";\r
  45                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  46 \r
  47                 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  48                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  49                 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
  50                 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
  51 \r
  52         }\r
  53 \r
  54         @Test()\r
  55         public void testCleanSequence() {\r
  56                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  57                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  58                                 SequenceUtil.cleanSequence(dirtySeq));\r
  59         }\r
  60 \r
  61         @Test()\r
  62         public void testDeepCleanSequence() {\r
  63                 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
  64                 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
  65                                 SequenceUtil.deepCleanSequence(dirtySeq));\r
  66         }\r
  67 \r
  68         @Test()\r
  69         public void testisProteinSequence() {\r
  70                 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
  71                 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
  72                 String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
  73                 assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
  74                 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
  75                 assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
  76                 AAseq += "XU";\r
  77                 assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
  78 \r
  79         }\r
  80 \r
  81         @Test()\r
  82         public void testReadWriteFasta() {\r
  83 \r
  84                 try {\r
  85                         FileInputStream fio = new FileInputStream(\r
  86                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
  87                         assertNotNull(fio);\r
  88                         List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
  89                         assertNotNull(fseqs);\r
  90                         assertEquals(3, fseqs.size());\r
  91                         assertEquals(3, fseqs.size());\r
  92                         fio.close();\r
  93                         FileOutputStream fou = new FileOutputStream(\r
  94                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
  95                         SequenceUtil.writeFasta(fou, fseqs);\r
  96                         fou.close();\r
  97                         FileOutputStream fou20 = new FileOutputStream(\r
  98                                         AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
  99                         SequenceUtil.writeFasta(fou20, fseqs, 21);\r
 100                         fou20.close();\r
 101 \r
 102                 } catch (FileNotFoundException e) {\r
 103                         e.printStackTrace();\r
 104                         fail(e.getLocalizedMessage());\r
 105                 } catch (IOException e) {\r
 106                         e.printStackTrace();\r
 107                         fail(e.getLocalizedMessage());\r
 108                 }\r
 109         }\r
 110 \r
 111         /**\r
 112          * This test tests the loading of horizontally formatted Jronn output file\r
 113          */\r
 114         @Test\r
 115         public void loadJronnFile() {\r
 116 \r
 117                 FileInputStream fio;\r
 118                 try {\r
 119                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
 120                         List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);\r
 121                         assertNotNull(aseqs);\r
 122                         assertEquals(aseqs.size(), 3);\r
 123                         AnnotatedSequence aseq = aseqs.get(0);\r
 124                         assertNotNull(aseq);\r
 125                         assertNotNull(aseq.getAnnotation());\r
 126                         // System.out.println(aseq);\r
 127                         assertEquals(aseq.getAnnotation().length, aseq.getSequence()\r
 128                                         .length());\r
 129                         fio.close();\r
 130                 } catch (FileNotFoundException e) {\r
 131                         e.printStackTrace();\r
 132                         fail(e.getLocalizedMessage());\r
 133                 } catch (IOException e) {\r
 134                         e.printStackTrace();\r
 135                         fail(e.getLocalizedMessage());\r
 136                 } catch (UnknownFileFormatException e) {\r
 137                         e.printStackTrace();\r
 138                         fail(e.getLocalizedMessage());\r
 139                 }\r
 140 \r
 141         }\r
 142 \r
 143         enum Trial {\r
 144                 one, two, three\r
 145         };\r
 146 \r
 147         /**\r
 148          * This test tests the loading of horizontally formatted Jronn output file\r
 149          */\r
 150         @SuppressWarnings("unchecked")\r
 151         @Test\r
 152         public void testMultiAnnotatedSequence() {\r
 153 \r
 154                 FileInputStream fio;\r
 155                 try {\r
 156                         fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 157                                         + "disembl.out");\r
 158                         List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil\r
 159                                         .readDisembl(fio);\r
 160                         assertNotNull(aseqs);\r
 161 \r
 162                         /*\r
 163                          * MultiAnnotatedSequence ma = new MultiAnnotatedSequence();\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 testReadResults() throws FileNotFoundException {\r
 185                 InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
 186                                 + "aacon_results.txt");\r
 187                 System.out.println(SequenceUtil.readResults(inStream));\r
 188         }\r
 189 }\r