testsrc/compbio/data/sequence/SequenceUtilTester.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.data.sequence;\r
  20 \r
  21 import static org.testng.AssertJUnit.assertEquals;\r
  22 import static org.testng.AssertJUnit.assertFalse;\r
  23 import static org.testng.AssertJUnit.assertNotNull;\r
  24 import static org.testng.AssertJUnit.assertTrue;\r
  25 import static org.testng.AssertJUnit.fail;\r
  26 \r
  27 import java.io.FileInputStream;\r
  28 import java.io.FileNotFoundException;\r
  29 import java.io.FileOutputStream;\r
  30 import java.io.IOException;\r
  31 import java.util.List;\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, 20);\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             List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);\r
 125             assertNotNull(aseqs);\r
 126             assertEquals(aseqs.size(), 3);\r
 127             AnnotatedSequence aseq = aseqs.get(0);\r
 128             assertNotNull(aseq);\r
 129             assertNotNull(aseq.getAnnotation());\r
 130             //System.out.println(aseq);\r
 131             assertEquals(aseq.getAnnotation().length, aseq.getSequence()\r
 132                     .length());\r
 133             fio.close();\r
 134         } catch (FileNotFoundException e) {\r
 135             e.printStackTrace();\r
 136             fail(e.getLocalizedMessage());\r
 137         } catch (IOException e) {\r
 138             e.printStackTrace();\r
 139             fail(e.getLocalizedMessage());\r
 140         } catch (UnknownFileFormatException e) {\r
 141             e.printStackTrace();\r
 142             fail(e.getLocalizedMessage());\r
 143         }\r
 144 \r
 145     }\r
 146 \r
 147 }\r