From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 9 Apr 2012 11:28:48 +0000 (+0200)
Subject: JAL-1067 - T-Coffee score file parser
X-Git-Tag: Archived_Release_2_7~4^2^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d63632f20b8c8c2961601b0ab22ecea92059240;p=jalview.git

JAL-1067 - T-Coffee score file parser
---

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
new file mode 100644
index 0000000..df00986
--- /dev/null
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -0,0 +1,352 @@
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A file parse for T-Coffee score ascii format. This file contains the alignment consensus 
+ * for each resude in any sequence.
+ * <p>
+ * This file is procuded by <code>t_coffee</code> providing the option 
+ * <code>-output=score_ascii </code> to the program command line
+ * 
+ * An example file is the following 
+ * 
+ * <pre>
+ * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+ * Cedric Notredame 
+ * CPU TIME:0 sec.
+ * SCORE=90
+ * *
+ *  BAD AVG GOOD
+ * *
+ * 1PHT   :  89
+ * 1BB9   :  90
+ * 1UHC   :  94
+ * 1YCS   :  94
+ * 1OOT   :  93
+ * 1ABO   :  94
+ * 1FYN   :  94
+ * 1QCF   :  94
+ * cons   :  90
+ * 
+ * 1PHT   999999999999999999999999998762112222543211112134
+ * 1BB9   99999999999999999999999999987-------4322----2234
+ * 1UHC   99999999999999999999999999987-------5321----2246
+ * 1YCS   99999999999999999999999999986-------4321----1-35
+ * 1OOT   999999999999999999999999999861-------3------1135
+ * 1ABO   99999999999999999999999999986-------422-------34
+ * 1FYN   99999999999999999999999999985-------32--------35
+ * 1QCF   99999999999999999999999999974-------2---------24
+ * cons   999999999999999999999999999851000110321100001134
+ * 
+ * 
+ * 1PHT   ----------5666642367889999999999889
+ * 1BB9   1111111111676653-355679999999999889
+ * 1UHC   ----------788774--66789999999999889
+ * 1YCS   ----------78777--356789999999999889
+ * 1OOT   ----------78877--356789999999997-67
+ * 1ABO   ----------687774--56779999999999889
+ * 1FYN   ----------6888842356789999999999889
+ * 1QCF   ----------6878742356789999999999889
+ * cons   00100000006877641356789999999999889
+ * </pre>
+ * 
+ * 
+ * @author Paolo Di Tommaso
+ *
+ */
+public class TCoffeeScoreFile {
+	
+	/** The {@link Header} structure holder */
+	Header header;
+	
+	/** 
+	 * Holds the consensues values for each sequences. It uses a LinkedHashMap to maintaint the 
+	 * insertion order. 
+	 */
+	LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
+	
+
+	/**
+	 * Get the string of score values for the specified seqeunce ID. 
+	 * @param id The sequence ID 
+	 * @return The scores as a string of values e.g. {@code 99999987-------432}. 
+	 * 	It return an empty string when the specified ID is missing. 
+	 */
+	public String getScoresFor( String id ) {
+		return scores.containsKey(id) ? scores.get(id).toString() : "";
+	}
+	
+	/**
+	 * @return The list of score string as a {@link List} object, in the same ordeer of the insertion i.e. in the MSA
+	 */
+	public List<String> getScoresList() {
+		List<String> result = new ArrayList<String>( scores.size() );
+		for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+			result.add(it.getValue().toString());
+		}
+		
+		return result;
+	}
+	
+	/**
+	 * @return The parsed score values a matrix of bytes
+	 */
+	public byte[][] getScoresArray() { 
+		byte[][] result = new byte[ scores.size() ][];
+		
+		int rowCount = 0;
+		for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+			String line = it.getValue().toString();
+			byte[] seqValues = new byte[ line.length() ];
+			for( int j=0, c=line.length(); j<c; j++ ) {
+				
+				byte val = (byte)(line.charAt(j) - '0');
+
+				seqValues[j] = ( val >= 0 && val <= 9 ) ? val : -1; 
+			}
+
+			result[rowCount++] = seqValues;
+		}
+		
+		return result;
+	}
+	
+	/**
+	 * Parse the specified file.
+	 * 
+	 * @param file The file to be parsed 
+	 */
+	public void parse(File file) {
+		try {
+			parse(new FileReader(file));
+		} 
+		catch (FileNotFoundException e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	/**
+	 * Parse the provided reader for the T-Coffee scores file format
+	 * 
+	 * @param reader 
+	 */
+	public void parse(Reader reader) {
+
+		try {
+			BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
+			doParsing(in);
+		}
+		catch( Exception e) {
+			throw new RuntimeException(e);
+		}
+	}
+	
+	private void doParsing(BufferedReader in) throws IOException {
+
+		/*
+		 * read the header
+		 */
+		header = readHeader(in);
+		
+		/*
+		 * initilize the structure
+		 */
+		for( Map.Entry<String,Integer> entry : header.scores.entrySet() ) {
+			scores.put( entry.getKey(), new StringBuilder());
+		}
+		
+		/*
+		 * go with the reading
+		 */
+		Block block;
+		while( (block = readBlock(in, header.scores.size())) != null  ) {
+			
+			/*
+			 * append sequences read in the block
+			 */
+			for( Map.Entry<String,String> entry : block.items.entrySet() ) {
+				StringBuilder scoreStringBuilder = scores.get(entry.getKey());
+				if( scoreStringBuilder == null ) {
+					throw new RuntimeException(String.format("Invalid T-Coffee score file. Sequence ID '%s' is not declared in header section", entry.getKey()));
+				}
+				
+				scoreStringBuilder.append( entry.getValue() );
+			}
+			
+		}
+		
+	}
+
+
+	static int parseInt( String str ) {
+		try {
+			return Integer.parseInt(str);
+		}
+		catch( NumberFormatException e ) {
+			// TODO report a warning ?
+			return 0;
+		}		
+	}
+	
+	/**
+	 * Reaad the header section in the T-Coffee score file format 
+	 * 
+	 * @param reader The scores reader 
+	 * @return The parser {@link Header} instance 
+	 * @throws RuntimeException when the header is not in the expected format
+	 */
+	static Header readHeader(BufferedReader reader) {
+		
+		Header result = null;
+		try {
+			result = new Header();
+			result.head = reader.readLine();
+			
+			String line;
+
+			while( (line = reader.readLine()) != null ) {
+				if( line.startsWith("SCORE=")) {
+					result.score = parseInt( line.substring(6).trim() );
+					break;
+				}
+			}
+
+			if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+			if( (line=reader.readLine())==null || !"BAD AVG GOOD".equals(line.trim())) return null;
+			if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+			
+			/*
+			 * now are expected a list if sequences ID up to the first blank line
+			 */
+			while( (line=reader.readLine()) != null ) {
+				if( "".equals(line) ) {
+					break;
+				}
+				
+				int p = line.indexOf(":");
+				if( p == -1 ) {
+					// TODO report a warning
+					continue;
+				}
+				
+				String id = line.substring(0,p).trim();
+				int val = parseInt(line.substring(p+1).trim());
+				if( "".equals(id) ) {
+					// TODO report warning
+					continue;
+				}
+				
+				result.scores.put(id,val);
+			}
+			
+		}
+		catch( IOException e ) {
+			throw new RuntimeException("Cannot parse T-Coffee score ascii file", e);
+		}
+		
+		return result;
+	} 
+	
+	/**
+	 * Read a scores block ihe provided stream. 
+	 * 
+	 * @param reader The stream to parse
+	 * @param size The expected number of the sequence to be read 
+	 * @return The {@link Block} instance read or {link null} null if the end of file has reached.
+	 * @throws IOException Something went wrong on the 'wire' 
+	 */
+	static Block readBlock( BufferedReader reader, int size ) throws IOException {
+		Block result = new Block(size);
+		String line;
+		
+		/*
+		 * read blank lines (eventually)
+		 */
+		while( (line=reader.readLine()) != null && "".equals(line.trim())) {
+			// consume blank lines 
+		}
+		
+		if( line == null ) return null;
+		
+		/*
+		 * read the scores block
+		 */
+		do {
+			if( "".equals(line.trim()) ) {
+				// terminated
+				break;
+			}
+			
+			// split the line on the first blank 
+			// the first part have to contain the sequence id
+			// theramining part are the scores values
+			int p = line.indexOf(" ");
+			if( p == -1 ) {
+				//TODO This is an unexpected condition, log a warning or throw an exception ? 
+				continue;
+			} 
+			
+			String id = line.substring(0,p).trim();
+			String val = line.substring(p+1).trim();
+			
+			result.items.put(id, val);
+			
+		} while( (line = reader.readLine()) != null ); 
+		
+
+		return result;
+	}
+
+	/*
+	 * The score file header 
+	 */
+	static class Header {
+		String head;
+		int score;
+
+		LinkedHashMap<String,Integer> scores = new LinkedHashMap<String,Integer>();
+		
+		public int getScoreAvg() { return score; }
+		
+		public int getScoreFor( String ID ) { 
+
+			return scores.containsKey(ID) ? scores.get(ID) : -1;
+	
+		}
+	}
+	
+	/*
+	 * Hold a single block values block in the score file
+	 */
+	static class Block {
+		int size;
+		Map<String,String> items;
+		
+		public Block( int size ) {
+			this.size = size;
+			this.items = new HashMap<String,String>(size);
+		} 
+	
+		String getScoresFor( String id ) {
+			return items.get(id);
+		}
+		
+		String getConsensus() {
+			return items.get("cons");
+		}
+	}
+	
+	
+
+}
diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
new file mode 100644
index 0000000..f654ba1
--- /dev/null
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -0,0 +1,140 @@
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.io.TCoffeeScoreFile.Block;
+import jalview.io.TCoffeeScoreFile.Header;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.List;
+
+import org.junit.Test;
+
+public class TCoffeeScoreFileTest {
+
+	final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+	
+	@Test
+	public void testReadHeader() throws FileNotFoundException {
+
+		Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+		assertNotNull(header);
+		assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
+		assertEquals( 90, header.score );
+		assertEquals( 89, header.getScoreFor("1PHT") );
+		assertEquals( 90, header.getScoreFor("1BB9") );
+		assertEquals( 94, header.getScoreFor("1UHC") );
+		assertEquals( 94, header.getScoreFor("1YCS") );
+		assertEquals( 93, header.getScoreFor("1OOT") );
+		assertEquals( 94, header.getScoreFor("1ABO") );
+		assertEquals( 94, header.getScoreFor("1FYN") );
+		assertEquals( 94, header.getScoreFor("1QCF") );
+		assertEquals( 90, header.getScoreFor("cons") );
+	}
+	
+	@Test
+	public void testReadBlock( ) throws IOException {
+		
+		String BLOCK = "\n" +
+				"\n" +
+				"\n" +
+				"1PHT   999999999999999999999999998762112222543211112134\n" +
+				"1BB9   99999999999999999999999999987-------4322----2234  \n" +
+				"1UHC   99999999999999999999999999987-------5321----2246\n" +
+				"1YCS   99999999999999999999999999986-------4321----1-35\n" +
+				"1OOT   999999999999999999999999999861-------3------1135  \n" +
+				"1ABO   99999999999999999999999999986-------422-------34\n" +
+				"1FYN   99999999999999999999999999985-------32--------35\n" +
+				"1QCF   99999999999999999999999999974-------2---------24\n" +
+				"cons   999999999999999999999999999851000110321100001134\n" +
+				"\n" +
+				"\n";
+		
+		Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
+		assertNotNull(block);
+		assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
+		assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
+		assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
+		assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
+		assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
+		assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
+		assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
+		assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
+		assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
+	}
+
+	@Test
+	public void testParse() throws FileNotFoundException {
+
+		TCoffeeScoreFile parser = new TCoffeeScoreFile();
+		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
+		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
+		assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
+		assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
+		assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
+		assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
+		assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
+		assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
+		assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );		
+	}
+
+	
+	@Test
+	public void testGetAsList() throws FileNotFoundException {
+		
+		TCoffeeScoreFile parser = new TCoffeeScoreFile();
+		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+		List<String> scores = parser.getScoresList();
+		assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
+		assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
+		assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
+		assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
+		assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
+		assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
+		assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
+		assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
+		assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );		
+		
+	} 
+	
+	
+	@Test
+	public void testGetAsArray() throws FileNotFoundException {
+		
+		TCoffeeScoreFile parser = new TCoffeeScoreFile();
+		parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+		byte[][] scores = parser.getScoresArray();
+	
+		assertEquals( 9, scores[0][0] );
+		assertEquals( 9, scores[1][0] );
+		assertEquals( 9, scores[2][0] );
+		assertEquals( 9, scores[3][0] );
+		assertEquals( 9, scores[4][0] );
+		assertEquals( 9, scores[5][0] );
+		assertEquals( 9, scores[6][0] );
+		assertEquals( 9, scores[7][0] );
+		assertEquals( 9, scores[8][0] );
+		
+		assertEquals( 5, scores[0][36] );
+		assertEquals( 4, scores[1][36] );
+		assertEquals( 5, scores[2][36] );
+		assertEquals( 4, scores[3][36] );
+		assertEquals( -1, scores[4][36] );
+		assertEquals( 4, scores[5][36] );
+		assertEquals( 3, scores[6][36] );
+		assertEquals( 2, scores[7][36] );
+		assertEquals( 3, scores[8][36] );
+		
+	} 
+	
+	
+	
+}
diff --git a/test/jalview/io/tcoffee.fasta_aln b/test/jalview/io/tcoffee.fasta_aln
new file mode 100644
index 0000000..63b12b1
--- /dev/null
+++ b/test/jalview/io/tcoffee.fasta_aln
@@ -0,0 +1,24 @@
+>1PHT
+YQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEI--
+--------GWLNGYNETTGERGDFPGTYVEYIG
+>1BB9
+FKVQAQHDYTATDTDELQLKAGDVVLVIP-------FQNP----EEQDEG
+WLMGVKESDWNQHK-ELEKCRGVFPENFTERVQ
+>1UHC
+QVYFAVYTFKARNPNELSVSANQKLKILE-------FKDV----TGNT--
+--------EWWLAE--VNGKKGYVPSNYIRKTE
+>1YCS
+GVIYALWDYEPQNDDELPMKEGDCMTIIH-------REDE----D-EI--
+--------EWWWA--RLNDKEGYVPRNLLGLYP
+>1OOT
+PKAVALYSFAGEESGDLPFRKGDVITILKK-------S------DSQN--
+--------DWWTG--RVNGREGIFPANYVE-LV
+>1ABO
+NLFVALYDFVASGDNTLSITKGEKLRVLG-------YNH-------NG--
+--------EWCEAQ--TKNGQGWVPSNYITPVN
+>1FYN
+TLFVALYDYEARTEDDLSFHKGEKFQILN-------SS--------EG--
+--------DWWEARSLTTGETGYIPSNYVAPVD
+>1QCF
+IIVVALYDYEAIHHEDLSFQKGDQMVVLE-------E---------SG--
+--------EWWKARSLATRKEGYIPSNYVARVD
\ No newline at end of file
diff --git a/test/jalview/io/tcoffee.score_ascii b/test/jalview/io/tcoffee.score_ascii
new file mode 100644
index 0000000..2b533a3
--- /dev/null
+++ b/test/jalview/io/tcoffee.score_ascii
@@ -0,0 +1,37 @@
+T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+Cedric Notredame 
+CPU TIME:0 sec.
+SCORE=90
+*
+ BAD AVG GOOD
+*
+1PHT   :  89
+1BB9   :  90
+1UHC   :  94
+1YCS   :  94
+1OOT   :  93
+1ABO   :  94
+1FYN   :  94
+1QCF   :  94
+cons   :  90
+
+1PHT   999999999999999999999999998762112222543211112134
+1BB9   99999999999999999999999999987-------4322----2234
+1UHC   99999999999999999999999999987-------5321----2246
+1YCS   99999999999999999999999999986-------4321----1-35
+1OOT   999999999999999999999999999861-------3------1135
+1ABO   99999999999999999999999999986-------422-------34
+1FYN   99999999999999999999999999985-------32--------35
+1QCF   99999999999999999999999999974-------2---------24
+cons   999999999999999999999999999851000110321100001134
+
+
+1PHT   ----------5666642367889999999999889
+1BB9   1111111111676653-355679999999999889
+1UHC   ----------788774--66789999999999889
+1YCS   ----------78777--356789999999999889
+1OOT   ----------78877--356789999999997-67
+1ABO   ----------687774--56779999999999889
+1FYN   ----------6888842356789999999999889
+1QCF   ----------6878742356789999999999889
+cons   00100000006877641356789999999999889