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