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