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
14 package compbio.data.sequence;
\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
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 import java.util.Map;
\r
30 import java.util.Set;
\r
32 import org.testng.annotations.Test;
\r
34 import compbio.metadata.AllTestSuit;
\r
36 public class SequenceUtilTester {
\r
39 public void testisNonAmbNucleotideSequence() {
\r
40 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";
\r
41 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));
\r
42 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";
\r
43 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));
\r
44 String nonDna = "atgfctgatgcatgcatgatgctga";
\r
45 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
47 nonDna = "atgc1tgatgcatgcatgatgctga";
\r
48 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
50 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
\r
51 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
52 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code
\r
53 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
\r
58 public void testCleanSequence() {
\r
59 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
\r
60 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
\r
61 SequenceUtil.cleanSequence(dirtySeq));
\r
65 public void testDeepCleanSequence() {
\r
66 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";
\r
67 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
\r
68 SequenceUtil.deepCleanSequence(dirtySeq));
\r
72 public void testisProteinSequence() {
\r
73 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
\r
74 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
\r
75 String notaSeq = "atgc1tgatgcatgcatgatgctga";
\r
76 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
\r
77 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
\r
78 assertTrue(SequenceUtil.isProteinSequence(AAseq));
\r
80 assertFalse(SequenceUtil.isProteinSequence(AAseq));
\r
85 public void testReadWriteFasta() {
\r
88 FileInputStream fio = new FileInputStream(
\r
89 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
\r
91 List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
\r
92 assertNotNull(fseqs);
\r
93 assertEquals(3, fseqs.size());
\r
94 assertEquals(3, fseqs.size());
\r
96 FileOutputStream fou = new FileOutputStream(
\r
97 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");
\r
98 SequenceUtil.writeFasta(fou, fseqs);
\r
100 FileOutputStream fou20 = new FileOutputStream(
\r
101 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
\r
102 SequenceUtil.writeFasta(fou20, fseqs, 21);
\r
105 } catch (FileNotFoundException e) {
\r
106 e.printStackTrace();
\r
107 fail(e.getLocalizedMessage());
\r
108 } catch (IOException e) {
\r
109 e.printStackTrace();
\r
110 fail(e.getLocalizedMessage());
\r
115 * This test tests the loading of horizontally formatted Jronn output file
\r
118 public void loadJronnFile() {
\r
120 FileInputStream fio;
\r
122 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
\r
123 Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);
\r
124 assertNotNull(aseqs);
\r
125 assertEquals(aseqs.size(), 3);
\r
126 Score aseq = aseqs.get("Foobar");
\r
127 assertNotNull(aseq);
\r
128 assertNotNull(aseq.getScores());
\r
129 // System.out.println(aseq);
\r
130 assertEquals(aseq.getScores().size(), aseq.getScores().size());
\r
132 } catch (FileNotFoundException e) {
\r
133 e.printStackTrace();
\r
134 fail(e.getLocalizedMessage());
\r
135 } catch (IOException e) {
\r
136 e.printStackTrace();
\r
137 fail(e.getLocalizedMessage());
\r
138 } catch (UnknownFileFormatException e) {
\r
139 e.printStackTrace();
\r
140 fail(e.getLocalizedMessage());
\r
150 * This test tests the loading of horizontally formatted Jronn output file
\r
152 @SuppressWarnings("unchecked")
\r
154 public void testMultiAnnotatedSequence() {
\r
156 FileInputStream fio;
\r
158 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
\r
160 Map<FastaSequence, Set<Score>> aseqs = SequenceUtil
\r
162 assertNotNull(aseqs);
\r
165 * Map<Trial, List<Number>> val = ma.getInstance(Trial.class);
\r
166 * List<Number> list = new ArrayList<Number>(); list.add(new
\r
167 * Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,
\r
168 * list); val.put(Trial.two, Arrays.asList(6.22f, 1, 37.6f));
\r
169 * System.out.println(val); AnnotatedSequence aseq = aseqs.get(0);
\r
172 } catch (FileNotFoundException e) {
\r
173 e.printStackTrace();
\r
174 fail(e.getLocalizedMessage());
\r
175 } catch (IOException e) {
\r
176 e.printStackTrace();
\r
177 fail(e.getLocalizedMessage());
\r
178 } catch (UnknownFileFormatException e) {
\r
179 e.printStackTrace();
\r
180 fail(e.getLocalizedMessage());
\r
185 public void testReadAAConResults() {
\r
187 InputStream inStream = new FileInputStream(
\r
188 AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");
\r
189 HashSet<Score> result = SequenceUtil.readAAConResults(inStream);
\r
191 assertNotNull(result);
\r
192 assertEquals(result.size(), 18);
\r
194 inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH
\r
195 + "aacon_result_single.out");
\r
196 result = SequenceUtil.readAAConResults(inStream);
\r
198 assertNotNull(result);
\r
199 assertEquals(result.size(), 1);
\r
200 assertEquals(result.iterator().next().getScores().size(), 568);
\r
201 } catch (IOException e) {
\r
202 e.printStackTrace();
\r
203 fail(e.getMessage());
\r