2 * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services
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3 * (JABAWS) @version: 1.0 This library is free software; you can redistribute it
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4 * and/or modify it under the terms of the Apache License version 2 as published
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5 * by the Apache Software Foundation This library is distributed in the hope
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6 * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
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7 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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8 * Apache License for more details. A copy of the license is in
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9 * apache_license.txt. It is also available here:
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10 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or
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11 * derived work distributed in source code form must include this copyright and
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14 package compbio.data.sequence;
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16 import static org.testng.AssertJUnit.assertEquals;
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17 import static org.testng.AssertJUnit.assertFalse;
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18 import static org.testng.AssertJUnit.assertNotNull;
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19 import static org.testng.AssertJUnit.assertTrue;
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20 import static org.testng.AssertJUnit.fail;
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22 import java.io.FileInputStream;
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23 import java.io.FileNotFoundException;
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24 import java.io.FileOutputStream;
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25 import java.io.IOException;
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26 import java.io.InputStream;
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27 import java.io.PrintWriter;
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28 import java.util.HashMap;
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29 import java.util.HashSet;
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30 import java.util.List;
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31 import java.util.Map;
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32 import java.util.Set;
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34 import org.testng.annotations.Test;
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36 import compbio.metadata.AllTestSuit;
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38 public class SequenceUtilTester {
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41 public void testisNonAmbNucleotideSequence() {
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42 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";
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43 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));
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44 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";
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45 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));
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46 String nonDna = "atgfctgatgcatgcatgatgctga";
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47 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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49 nonDna = "atgc1tgatgcatgcatgatgctga";
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50 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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52 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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53 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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54 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code
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55 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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60 public void testCleanSequence() {
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61 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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62 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
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63 SequenceUtil.cleanSequence(dirtySeq));
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67 public void testDeepCleanSequence() {
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68 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";
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69 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
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70 SequenceUtil.deepCleanSequence(dirtySeq));
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74 public void testisProteinSequence() {
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75 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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76 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
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77 String notaSeq = "atgc1tgatgcatgcatgatgctga";
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78 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
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79 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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80 assertTrue(SequenceUtil.isProteinSequence(AAseq));
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82 assertFalse(SequenceUtil.isProteinSequence(AAseq));
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87 public void testCleanProteinSequence() {
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88 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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89 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
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90 // This will still be NON protein sequence despite having only correct
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91 // letters because the letters match perfectly the nucleotide sequence!
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92 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil
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93 .cleanProteinSequence(dirtySeq)));
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95 String notaSeq = "atgc1tgatgcatgcatgatgmctga";
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96 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
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97 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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98 .cleanProteinSequence(notaSeq)));
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100 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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101 assertTrue(SequenceUtil.isProteinSequence(AAseq));
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102 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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103 .cleanProteinSequence(AAseq)));
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106 assertFalse(SequenceUtil.isProteinSequence(AAseq));
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107 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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108 .cleanProteinSequence(AAseq)));
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112 public void testReadWriteFasta() {
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115 FileInputStream fio = new FileInputStream(
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116 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
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117 assertNotNull(fio);
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118 List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
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119 assertNotNull(fseqs);
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120 assertEquals(3, fseqs.size());
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121 assertEquals(3, fseqs.size());
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123 FileOutputStream fou = new FileOutputStream(
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124 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");
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125 SequenceUtil.writeFasta(fou, fseqs);
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127 FileOutputStream fou20 = new FileOutputStream(
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128 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
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129 SequenceUtil.writeFasta(fou20, fseqs, 21);
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132 } catch (FileNotFoundException e) {
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133 e.printStackTrace();
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134 fail(e.getLocalizedMessage());
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135 } catch (IOException e) {
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136 e.printStackTrace();
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137 fail(e.getLocalizedMessage());
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142 * This test tests the loading of horizontally formatted Jronn output file
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145 public void loadJronnFile() {
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147 FileInputStream fio;
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149 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
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150 Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);
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151 assertNotNull(aseqs);
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152 assertEquals(aseqs.size(), 3);
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153 Score aseq = aseqs.get("Foobar");
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154 assertNotNull(aseq);
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155 assertNotNull(aseq.getScores());
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156 // System.out.println(aseq);
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157 assertEquals(aseq.getScores().size(), aseq.getScores().size());
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159 } catch (FileNotFoundException e) {
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160 e.printStackTrace();
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161 fail(e.getLocalizedMessage());
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162 } catch (IOException e) {
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163 e.printStackTrace();
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164 fail(e.getLocalizedMessage());
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165 } catch (UnknownFileFormatException e) {
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166 e.printStackTrace();
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167 fail(e.getLocalizedMessage());
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177 * This test tests the loading of horizontally formatted Jronn output file
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181 * M 0.86010 0.88512 0.37094
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183 * T 0.79983 0.85864 0.44331
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186 @SuppressWarnings("unchecked")
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188 public void testReadDisemblResults() {
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190 FileInputStream fio;
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192 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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194 Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);
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195 assertNotNull(aseqs);
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196 assertEquals(aseqs.size(), 3);
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197 ScoreManager sman = ScoreManager.newInstance(aseqs);
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199 for (String fs : aseqs.keySet()) {
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200 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "
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202 Set<Score> scores = aseqs.get(fs);
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203 assertEquals(scores.size(), 3);
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206 } catch (FileNotFoundException e) {
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207 e.printStackTrace();
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208 fail(e.getLocalizedMessage());
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209 } catch (IOException e) {
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210 e.printStackTrace();
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211 fail(e.getLocalizedMessage());
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212 } catch (UnknownFileFormatException e) {
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213 e.printStackTrace();
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214 fail(e.getLocalizedMessage());
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219 * This test tests the loading of horizontally formatted Jronn output file
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223 * >Foobar_dundeefriends
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225 * # GlobDoms 2-358, 373-568
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227 * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481
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229 * # RESIDUE DYDX RAW SMOOTHED
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231 * M 0.0044 -0.2259 -0.2259
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233 * T -0.1308 -0.2170 -0.2170
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237 * > Second sequence
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239 @SuppressWarnings("unchecked")
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241 public void testReadGlobPlotResults() {
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243 FileInputStream fio;
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245 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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247 HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);
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248 assertNotNull(aseqs);
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249 assertEquals(aseqs.size(), 3);
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251 String fsdf = null;
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252 Set<Score> scores = null;
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253 for (String fs : aseqs.keySet()) {
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254 if ("Foobar_dundeefriends".contains(fs)) {
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256 scores = aseqs.get(fs);
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258 assertEquals(scores.size(), 5);
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261 ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);
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262 sm.writeOut(new PrintWriter(System.out, true));
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264 for (Score score : scores) {
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266 if (score.getMethod()
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267 .equals(GlobProtResult.Disorder.toString())) {
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268 assertEquals(score.getRanges().size(), 7);
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269 assertTrue(score.getScores().isEmpty());
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271 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {
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272 assertFalse(score.getScores().isEmpty());
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273 assertTrue(score.getRanges().isEmpty());
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277 } catch (FileNotFoundException e) {
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278 e.printStackTrace();
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279 fail(e.getLocalizedMessage());
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280 } catch (IOException e) {
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281 e.printStackTrace();
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282 fail(e.getLocalizedMessage());
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283 } catch (UnknownFileFormatException e) {
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284 e.printStackTrace();
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285 fail(e.getLocalizedMessage());
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290 public void testReadAAConResults() {
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292 InputStream inStream = new FileInputStream(
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293 AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");
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294 HashSet<Score> result = SequenceUtil.readAAConResults(inStream);
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296 assertNotNull(result);
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297 assertEquals(result.size(), 18);
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299 inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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300 + "aacon_result_single.out");
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301 result = SequenceUtil.readAAConResults(inStream);
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303 assertNotNull(result);
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304 assertEquals(result.size(), 1);
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305 assertEquals(result.iterator().next().getScores().size(), 568);
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306 } catch (IOException e) {
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307 e.printStackTrace();
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308 fail(e.getMessage());
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