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.File;
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23 import java.io.FileInputStream;
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24 import java.io.FileNotFoundException;
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25 import java.io.FileOutputStream;
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26 import java.io.IOException;
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27 import java.io.InputStream;
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28 import java.io.PrintWriter;
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29 import java.util.HashMap;
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30 import java.util.HashSet;
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31 import java.util.List;
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32 import java.util.Map;
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33 import java.util.Set;
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35 import org.testng.annotations.Test;
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37 import compbio.metadata.AllTestSuit;
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38 import compbio.runner.disorder.Disembl;
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40 public class SequenceUtilTester {
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43 public void testisNonAmbNucleotideSequence() {
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44 String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";
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45 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));
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46 String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";
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47 assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));
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48 String nonDna = "atgfctgatgcatgcatgatgctga";
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49 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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51 nonDna = "atgc1tgatgcatgcatgatgctga";
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52 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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54 nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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55 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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56 // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code
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57 assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));
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62 public void testCleanSequence() {
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63 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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64 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
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65 SequenceUtil.cleanSequence(dirtySeq));
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69 public void testDeepCleanSequence() {
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70 String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";
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71 assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),
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72 SequenceUtil.deepCleanSequence(dirtySeq));
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76 public void testisProteinSequence() {
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77 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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78 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
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79 String notaSeq = "atgc1tgatgcatgcatgatgctga";
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80 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
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81 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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82 assertTrue(SequenceUtil.isProteinSequence(AAseq));
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84 assertFalse(SequenceUtil.isProteinSequence(AAseq));
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89 public void testCleanProteinSequence() {
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90 String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";
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91 assertFalse(SequenceUtil.isProteinSequence(dirtySeq));
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92 // This will still be NON protein sequence despite having only correct
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93 // letters because the letters match perfectly the nucleotide sequence!
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94 assertFalse(SequenceUtil.isProteinSequence(SequenceUtil
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95 .cleanProteinSequence(dirtySeq)));
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97 String notaSeq = "atgc1tgatgcatgcatgatgmctga";
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98 assertFalse(SequenceUtil.isProteinSequence(notaSeq));
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99 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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100 .cleanProteinSequence(notaSeq)));
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102 String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";
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103 assertTrue(SequenceUtil.isProteinSequence(AAseq));
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104 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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105 .cleanProteinSequence(AAseq)));
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108 assertFalse(SequenceUtil.isProteinSequence(AAseq));
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109 assertTrue(SequenceUtil.isProteinSequence(SequenceUtil
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110 .cleanProteinSequence(AAseq)));
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114 public void testReadWriteFasta() {
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117 FileInputStream fio = new FileInputStream(
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118 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
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119 assertNotNull(fio);
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120 List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
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121 assertNotNull(fseqs);
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122 assertEquals(3, fseqs.size());
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123 assertEquals(3, fseqs.size());
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125 FileOutputStream fou = new FileOutputStream(
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126 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");
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127 SequenceUtil.writeFasta(fou, fseqs);
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129 FileOutputStream fou20 = new FileOutputStream(
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130 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");
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131 SequenceUtil.writeFasta(fou20, fseqs, 21);
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134 } catch (FileNotFoundException e) {
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135 e.printStackTrace();
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136 fail(e.getLocalizedMessage());
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137 } catch (IOException e) {
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138 e.printStackTrace();
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139 fail(e.getLocalizedMessage());
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143 // Potential Bug :- Sequence names are shortened to 2-3 letters
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145 public void testReadFastaWriteClustal() {
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148 FileInputStream fio = new FileInputStream(
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149 AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");
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150 assertNotNull(fio);
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151 List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);
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152 assertNotNull(fseqs);
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155 char gapChar = '-';
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156 FileOutputStream fou = new FileOutputStream(
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157 AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");
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158 SequenceUtil.writeClustal(fou, fseqs, gapChar);
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161 } catch (FileNotFoundException e) {
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162 e.printStackTrace();
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163 fail(e.getLocalizedMessage());
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164 } catch (IOException e) {
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165 e.printStackTrace();
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166 fail(e.getLocalizedMessage());
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175 * This test tests the loading of horizontally formatted Jronn output file
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178 public void loadJronnFile() {
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180 FileInputStream fio;
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182 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");
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183 Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);
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184 assertNotNull(aseqs);
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185 assertEquals(aseqs.size(), 3);
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186 Score aseq = aseqs.get("Foobar");
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187 assertNotNull(aseq);
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188 assertNotNull(aseq.getScores());
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189 // System.out.println(aseq);
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190 assertEquals(aseq.getScores().size(), aseq.getScores().size());
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192 } catch (FileNotFoundException e) {
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193 e.printStackTrace();
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194 fail(e.getLocalizedMessage());
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195 } catch (IOException e) {
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196 e.printStackTrace();
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197 fail(e.getLocalizedMessage());
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198 } catch (UnknownFileFormatException e) {
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199 e.printStackTrace();
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200 fail(e.getLocalizedMessage());
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210 * This test tests the loading of horizontally formatted Jronn output file
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214 * M 0.86010 0.88512 0.37094
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216 * T 0.79983 0.85864 0.44331
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219 @SuppressWarnings("unchecked")
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221 public void testReadDisemblResults() {
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224 Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();
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225 Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();
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226 Map<String,Map<String, Float>> _values=new HashMap<String, Map<String,Float>>();
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227 Map<String, Float> values = new HashMap<String, Float>();
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229 rset = new HashSet<Range>();
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230 for (String[] se:new String[][] { { "34","41"},{"50","58"},{"83","91"},{"118","127"},{" 160","169"},{" 191","220"},{" 243","252"},{" 287","343"},{" 350","391"},{" 429","485"},{" 497","506"},{"539","547"}})
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232 rset.add(new Range(se));
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234 ranges.put(DisemblResult.COILS.toString(), rset);
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235 values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));
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236 rset = new HashSet<Range>();
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237 for (String[] se:new String[][] { { "355","368"}})
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239 rset.add(new Range(se));
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241 ranges.put(DisemblResult.REM465.toString(), rset);
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242 values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));
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243 rset = new HashSet<Range>();
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244 for (String[] se:new String[][] { { "190","204"}})
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246 rset.add(new Range(se));
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248 ranges.put(DisemblResult.HOTLOOPS.toString(), rset);
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249 values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));
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250 _ranges.put("Foobar_dundeefriends", ranges);
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251 _values.put("Foobar_dundeefriends", values);
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252 FileInputStream fio;
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254 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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256 Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);
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257 assertNotNull(aseqs);
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258 assertEquals(aseqs.size(), 3);
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259 ScoreManager sman = ScoreManager.newInstance(aseqs);
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261 for (String fs : aseqs.keySet()) {
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262 assertTrue(" Foobar_dundeefriends Foobar dundeefriends "
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264 Set<Score> scores = aseqs.get(fs);
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265 assertEquals(scores.size(), 3);
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266 for (Score sc:scores) {
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267 if (_ranges.containsKey(fs))
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269 assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());
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270 assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));
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275 } catch (FileNotFoundException e) {
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276 e.printStackTrace();
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277 fail(e.getLocalizedMessage());
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278 } catch (IOException e) {
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279 e.printStackTrace();
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280 fail(e.getLocalizedMessage());
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281 } catch (UnknownFileFormatException e) {
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282 e.printStackTrace();
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283 fail(e.getLocalizedMessage());
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287 * This test tests the loading of horizontally formatted Jronn output file
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291 * >Foobar_dundeefriends
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293 * # GlobDoms 2-358, 373-568
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295 * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481
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297 * # RESIDUE DYDX RAW SMOOTHED
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299 * M 0.0044 -0.2259 -0.2259
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301 * T -0.1308 -0.2170 -0.2170
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305 * > Second sequence
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307 @SuppressWarnings("unchecked")
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309 public void testReadGlobPlotResults() {
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311 FileInputStream fio;
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313 fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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315 HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);
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316 assertNotNull(aseqs);
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317 assertEquals(aseqs.size(), 3);
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319 String fsdf = null;
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320 Set<Score> scores = null;
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321 for (String fs : aseqs.keySet()) {
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322 if ("Foobar_dundeefriends".contains(fs)) {
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324 scores = aseqs.get(fs);
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326 assertEquals(scores.size(), 5);
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329 ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);
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330 sm.writeOut(new PrintWriter(System.out, true));
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332 for (Score score : scores) {
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334 if (score.getMethod()
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335 .equals(GlobProtResult.Disorder.toString())) {
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336 assertEquals(score.getRanges().size(), 7);
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337 assertTrue(score.getScores().isEmpty());
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339 if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {
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340 assertFalse(score.getScores().isEmpty());
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341 assertTrue(score.getRanges().isEmpty());
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345 } catch (FileNotFoundException e) {
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346 e.printStackTrace();
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347 fail(e.getLocalizedMessage());
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348 } catch (IOException e) {
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349 e.printStackTrace();
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350 fail(e.getLocalizedMessage());
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351 } catch (UnknownFileFormatException e) {
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352 e.printStackTrace();
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353 fail(e.getLocalizedMessage());
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358 public void testReadIUPredForShortAndLongDisorder() {
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360 Map<String, Score> scores = SequenceUtil.readIUPred(new File(
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361 AllTestSuit.TEST_DATA_PATH, "out.long"));
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362 ScoreManager man = ScoreManager.newInstanceSingleScore(scores);
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363 // man.writeOut(new PrintWriter(System.out, true));
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364 assertNotNull(scores);
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365 assertEquals(3, scores.size());
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367 Score score = scores.get("Foobar_dundeefriends");
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368 assertNotNull(score);
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369 assertEquals(0, score.getRanges().size());
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370 assertEquals(568, score.getScores().size());
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371 assertEquals("Long", score.getMethod());
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373 score = scores.get("Foobar");
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374 assertNotNull(score);
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375 assertEquals(0, score.getRanges().size());
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376 assertEquals(481, score.getScores().size());
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377 assertEquals("Long", score.getMethod());
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379 score = scores.get("dundeefriends");
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380 assertNotNull(score);
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381 assertEquals(0, score.getRanges().size());
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382 assertEquals(513, score.getScores().size());
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383 assertEquals("Long", score.getMethod());
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385 } catch (IOException e) {
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386 e.printStackTrace();
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387 fail(e.getLocalizedMessage());
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388 } catch (UnknownFileFormatException e) {
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389 e.printStackTrace();
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390 fail(e.getLocalizedMessage());
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395 public void testReadIUPredForGlobDomain() {
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397 Map<String, Score> scores = SequenceUtil.readIUPred(new File(
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398 AllTestSuit.TEST_DATA_PATH, "output.glob"));
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399 assertNotNull(scores);
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400 assertEquals(2, scores.size());
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401 ScoreManager man = ScoreManager.newInstanceSingleScore(scores);
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402 // man.writeOut(new PrintWriter(System.out, true));
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403 assertEquals(2, man.getNumberOfSeq());
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404 Score score = scores.get("P53_HUMA");
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405 assertNotNull(score);
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406 assertEquals(2, score.getRanges().size());
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407 assertEquals(0, score.getScores().size());
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408 assertEquals("Glob", score.getMethod());
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410 score = scores.get("Foobar_dundeefriends");
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411 assertEquals(0, score.getRanges().size());
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412 } catch (IOException e) {
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413 e.printStackTrace();
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414 fail(e.getLocalizedMessage());
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415 } catch (UnknownFileFormatException e) {
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416 e.printStackTrace();
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417 fail(e.getLocalizedMessage());
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421 public void testReadAAConResults() {
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423 InputStream inStream = new FileInputStream(
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424 AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");
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425 HashSet<Score> result = SequenceUtil.readAAConResults(inStream);
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427 assertNotNull(result);
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428 assertEquals(result.size(), 18);
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430 inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH
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431 + "aacon_result_single.out");
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432 result = SequenceUtil.readAAConResults(inStream);
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434 assertNotNull(result);
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435 assertEquals(result.size(), 1);
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436 assertEquals(result.iterator().next().getScores().size(), 568);
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437 } catch (IOException e) {
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438 e.printStackTrace();
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439 fail(e.getMessage());
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