-/*\r
- * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
- * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
- * and/or modify it under the terms of the Apache License version 2 as published\r
+/* Copyright (c) 2009 Peter Troshin\r
+ * Copyright (c) 2013 Alexander Sherstnev\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) \r
+ * @version: 2.5\r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under \r
+ * the terms of the Apache License version 2 as published\r
* by the Apache Software Foundation This library is distributed in the hope\r
* that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
* warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
* Apache License for more details. A copy of the license is in\r
* apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
- * derived work distributed in source code form must include this copyright and\r
- * license notice.\r
+ * \r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
+ * \r
+ * Any republication or derived work distributed in source code form must include \r
+ * this copyright and license notice.\r
*/\r
package compbio.data.sequence;\r
\r
import static org.testng.AssertJUnit.assertTrue;\r
import static org.testng.AssertJUnit.fail;\r
\r
+import java.io.File;\r
import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.InputStream;\r
+import java.io.PrintWriter;\r
+import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
import java.util.Map;\r
public class SequenceUtilTester {\r
\r
@Test()\r
- public void testisNonAmbNucleotideSequence() {\r
+ public void isNonAmbNucleotideSequence() {\r
String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
// String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
}\r
\r
@Test()\r
- public void testCleanSequence() {\r
+ public void CleanSequence() {\r
String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
- SequenceUtil.cleanSequence(dirtySeq));\r
+ assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.cleanSequence(dirtySeq));\r
}\r
\r
@Test()\r
- public void testDeepCleanSequence() {\r
+ public void DeepCleanSequence() {\r
String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),\r
- SequenceUtil.deepCleanSequence(dirtySeq));\r
+ assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.deepCleanSequence(dirtySeq));\r
}\r
\r
@Test()\r
- public void testisProteinSequence() {\r
+ public void isProteinSequence() {\r
String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
}\r
\r
@Test()\r
- public void testReadWriteFasta() {\r
+ public void CleanProteinSequence() {\r
+ String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
+ assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
+ // This will still be NON protein sequence despite having only correct\r
+ // letters because the letters match perfectly the nucleotide sequence!\r
+ assertFalse(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(dirtySeq)));\r
+\r
+ String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
+ assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(notaSeq)));\r
+\r
+ String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
+ assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
+ AAseq += "XU";\r
\r
+ assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
+ assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
+ }\r
+\r
+ @Test()\r
+ public void ReadWriteFasta() {\r
try {\r
- FileInputStream fio = new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
+ FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
assertNotNull(fio);\r
List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
assertNotNull(fseqs);\r
assertEquals(3, fseqs.size());\r
assertEquals(3, fseqs.size());\r
fio.close();\r
- FileOutputStream fou = new FileOutputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
+ FileOutputStream fou = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
SequenceUtil.writeFasta(fou, fseqs);\r
fou.close();\r
- FileOutputStream fou20 = new FileOutputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
+ FileOutputStream fou20 = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
SequenceUtil.writeFasta(fou20, fseqs, 21);\r
fou20.close();\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
\r
+ // Potential Bug :- Sequence names are shortened to 2-3 letters\r
+ @Test\r
+ public void testReadFastaWriteClustal() {\r
+ \r
+ try {\r
+ FileInputStream fio = new FileInputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
+ assertNotNull(fio);\r
+ List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
+ assertNotNull(fseqs);\r
+ fio.close();\r
+ \r
+ char gapChar = '-';\r
+ FileOutputStream fou = new FileOutputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");\r
+ SequenceUtil.writeClustal(fou, fseqs, gapChar);\r
+ fou.close();\r
+ \r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
* This test tests the loading of horizontally formatted Jronn output file\r
*/\r
@Test\r
- public void loadJronnFile() {\r
+ public void LoadJronnFile() {\r
\r
FileInputStream fio;\r
try {\r
Score aseq = aseqs.get("Foobar");\r
assertNotNull(aseq);\r
assertNotNull(aseq.getScores());\r
- // System.out.println(aseq);\r
assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
fio.close();\r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
-\r
}\r
\r
enum Trial {\r
/**\r
* This test tests the loading of horizontally formatted Jronn output file\r
* \r
- * First seq \r
+ * First seq\r
* \r
- * M 0.86010 0.88512 0.37094\r
+ * M 0.86010 0.88512 0.37094\r
* \r
- * T 0.79983 0.85864 0.44331\r
+ * T 0.79983 0.85864 0.44331\r
* \r
*/\r
@SuppressWarnings("unchecked")\r
@Test\r
- public void testReadDisemblResults() {\r
+ public void ReadDisemblResults() {\r
+ Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
+ Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
+ Map<String,Map<String, Float>> _values=new HashMap<String, Map<String,Float>>();\r
+ Map<String, Float> values = new HashMap<String, Float>();\r
+ Set<Range> rset;\r
+ rset = new HashSet<Range>();\r
+ 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"}}) {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.COILS.toString(), rset);\r
+ values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
+ rset = new HashSet<Range>();\r
+ for (String[] se:new String[][] { { "355","368"}}) {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.REM465.toString(), rset);\r
+ values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
+ rset = new HashSet<Range>();\r
+ for (String[] se:new String[][] { { "190","204"}}) {\r
+ rset.add(new Range(se));\r
+ }\r
+ ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
+ values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
+ _ranges.put("Foobar_dundeefriends", ranges);\r
+ _values.put("Foobar_dundeefriends", values);\r
+ FileInputStream fio;\r
+ try {\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "disembl.out");\r
+ Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
+ assertNotNull(aseqs);\r
+ assertEquals(aseqs.size(), 3);\r
+ ScoreManager sman = ScoreManager.newInstance(aseqs);\r
+\r
+ for (String fs : aseqs.keySet()) {\r
+ assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs));\r
+ Set<Score> scores = aseqs.get(fs);\r
+ assertEquals(scores.size(), 3);\r
+ for (Score sc:scores) {\r
+ if (_ranges.containsKey(fs)) {\r
+ assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
+ assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
+ }\r
+ }\r
+ }\r
+ fio.close();\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (UnknownFileFormatException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * This method tests the loading of horizontally formatted Jronn output file\r
+ * \r
+ * First sequence:\r
+ * \r
+ * >Foobar_dundeefriends\r
+ * \r
+ * # GlobDoms 2-358, 373-568\r
+ * \r
+ * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
+ * \r
+ * # RESIDUE DYDX RAW SMOOTHED\r
+ * \r
+ * M 0.0044 -0.2259 -0.2259\r
+ * \r
+ * T -0.1308 -0.2170 -0.2170\r
+ * \r
+ * ............\r
+ * \r
+ * > Second sequence\r
+ */\r
+ @SuppressWarnings("unchecked")\r
+ @Test\r
+ public void ReadGlobPlotResults() {\r
\r
FileInputStream fio;\r
try {\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
- + "scores.out");\r
- Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
- .readDisembl(fio);\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "globplot.out");\r
+ HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
assertNotNull(aseqs);\r
- assertEquals(aseqs.size(), 3); \r
- System.out.println(aseqs);\r
- for(FastaSequence fs: aseqs.keySet()) {\r
- assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs.getId()));\r
- Set<Score> scores = aseqs.get(fs); \r
- assertEquals(scores.size(),3);\r
+ assertEquals(aseqs.size(), 3);\r
+\r
+ String fsdf = null;\r
+ Set<Score> scores = null;\r
+ for (String fs : aseqs.keySet()) {\r
+ if ("Foobar_dundeefriends".contains(fs)) {\r
+ fsdf = fs;\r
+ scores = aseqs.get(fs);\r
+ }\r
+ assertEquals(scores.size(), 5);\r
}\r
- fio.close();\r
+\r
+ ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
+ sm.writeOut(new PrintWriter(System.out, true));\r
+\r
+ for (Score score : scores) {\r
+ if (score.getMethod().equals(GlobProtResult.Disorder.toString())) {\r
+ assertEquals(score.getRanges().size(), 7);\r
+ assertTrue(score.getScores().isEmpty());\r
+ }\r
+ if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
+ assertFalse(score.getScores().isEmpty());\r
+ assertTrue(score.getRanges().isEmpty());\r
+ }\r
+ }\r
+ fio.close();\r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
\r
@Test\r
- public void testReadAAConResults() {\r
+ public void ReadIUPredForShortAndLongDisorder() {\r
try {\r
- InputStream inStream = new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
+ Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "out.long"));\r
+ ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
+ assertNotNull(scores);\r
+ assertEquals(3, scores.size());\r
+\r
+ Score score = scores.get("Foobar_dundeefriends");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(568, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+\r
+ score = scores.get("Foobar");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(481, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+\r
+ score = scores.get("dundeefriends");\r
+ assertNotNull(score);\r
+ assertEquals(0, score.getRanges().size());\r
+ assertEquals(513, score.getScores().size());\r
+ assertEquals("Long", score.getMethod());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (UnknownFileFormatException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test\r
+ public void ReadIUPredForGlobDomain() {\r
+ try {\r
+ Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
+ assertNotNull(scores);\r
+ assertEquals(2, scores.size());\r
+ ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
+ assertEquals(2, man.getNumberOfSeq());\r
+ Score score = scores.get("P53_HUMA");\r
+ assertNotNull(score);\r
+ assertEquals(2, score.getRanges().size());\r
+ assertEquals(0, score.getScores().size());\r
+ assertEquals("Glob", score.getMethod());\r
+ score = scores.get("Foobar_dundeefriends");\r
+ assertEquals(0, score.getRanges().size());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (UnknownFileFormatException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test\r
+ public void ReadAAConResults() {\r
+ try {\r
+ InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
inStream.close();\r
assertNotNull(result);\r
assertEquals(result.size(), 18);\r
\r
- inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
- + "aacon_result_single.out");\r
+ inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_result_single.out");\r
result = SequenceUtil.readAAConResults(inStream);\r
inStream.close();\r
assertNotNull(result);\r
fail(e.getMessage());\r
}\r
}\r
+ @Test\r
+ public void ReadJpredResults() {\r
+ try {\r
+ InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");\r
+ List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);\r
+ inStream.close();\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 19);\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
}\r
+\r
git://source.jalview.org / jabaws.git / blobdiff