From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Wed, 27 Apr 2011 23:10:25 +0000 (+0000)
Subject: New FastaReader implementing iterator & test case for it
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=26166c1ca1dd3761305024cef6ee6ae67c6c135f;p=jabaws.git

New FastaReader implementing iterator & test case for it

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4041 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
new file mode 100644
index 0000000..10eec8f
--- /dev/null
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -0,0 +1,123 @@
+package compbio.data.sequence;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Iterator;
+import java.util.Scanner;
+
+import compbio.util.Util;
+
+/**
+ * Reads files with FASTA formatted sequences. All the information in the FASTA
+ * header is preserved including trailing white spaces. All the white spaces are
+ * removed from the sequence.
+ * 
+ * Examples of the correct input:
+ * 
+ * <pre>
+ * 
+ * >zedpshvyzg
+ * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
+ * 
+ * >xovkactesa
+ * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
+ * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
+ * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
+ * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
+ * 
+ * >ntazzewyvv
+ * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
+ * EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG	
+ * EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW 
+ *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
+ *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
+ *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
+ * 
+ *    > 12 d t y wi 		k	jbke  	
+ *   KLSHHDCD
+ *    N
+ *     H
+ *     HSKCTEPHCGNSHQMLHRDP
+ *     CCDQCQSWEAENWCASMRKAILF
+ * 
+ * </pre>
+ * 
+ * @author Peter Troshin
+ * @version 1.0 April 2011
+ * 
+ */
+public class FastaReader implements Iterator<FastaSequence> {
+
+	private final Scanner input;
+
+	/**
+	 * Header data can contain non-ASCII symbols and read in UTF8
+	 * 
+	 * @param input
+	 *            the file containing the list of FASTA formatted sequences to
+	 *            read from
+	 * @throws FileNotFoundException
+	 *             if the input file is not found
+	 */
+	public FastaReader(final String input) throws FileNotFoundException {
+		this.input = new Scanner(new File(input), "UTF8");
+		this.input.useDelimiter("\\s*>");
+	}
+
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	public boolean hasNext() {
+		return input.hasNext();
+	}
+
+	/**
+	 * Reads the next FastaSequence from the input
+	 * 
+	 * @throws AssertionError
+	 *             if the header or the sequence is missing
+	 */
+	@Override
+	public FastaSequence next() {
+		return FastaReader.toFastaSequence(input.next());
+	}
+
+	/**
+	 * Not implemented
+	 */
+	@Override
+	public void remove() {
+		throw new UnsupportedOperationException();
+	}
+
+	private static FastaSequence toFastaSequence(final String singleFastaEntry) {
+		final Scanner sc = new Scanner(singleFastaEntry);
+		// Use new line delimiter
+		sc.useDelimiter("\n");
+		if (!sc.hasNext()) {
+			throw new AssertionError(
+					"The FASTA sequence must contain the header information"
+							+ " separated by the new line from the sequence. Given sequence does not appear to "
+							+ "contain the header! Given data:\n "
+							+ singleFastaEntry);
+		}
+		String header = sc.next();
+		// Get rid of the new line chars (should cover common cases)
+		header = header.replaceAll("\n", "").replaceAll("\r", "");
+
+		sc.useDelimiter("\\s*");
+		final StringBuilder sb = new StringBuilder();
+		while (sc.hasNext()) {
+			sb.append(sc.next().trim());
+		}
+		final String sequence = sb.toString();
+		if (Util.isEmpty(sequence)) {
+			throw new AssertionError(
+					"Empty sequences are not allowed! Please make sure the "
+							+ " data is in the FASTA format! Given data:\n "
+							+ singleFastaEntry);
+		}
+		return new FastaSequence(header, sequence);
+	}
+}
diff --git a/testsrc/compbio/data/sequence/FastaReaderTester.java b/testsrc/compbio/data/sequence/FastaReaderTester.java
new file mode 100644
index 0000000..77a7fd5
--- /dev/null
+++ b/testsrc/compbio/data/sequence/FastaReaderTester.java
@@ -0,0 +1,73 @@
+package compbio.data.sequence;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import compbio.metadata.AllTestSuit;
+
+public class FastaReaderTester {
+
+	static FastaSequence s0 = new FastaSequence(
+			"zedpshvyzg",
+			"GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD");
+
+	static FastaSequence s1 = new FastaSequence(
+			"xovkactesa",
+			"CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM"
+					+ "FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG"
+					+ "FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH"
+					+ "DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC");
+	static FastaSequence s2 = new FastaSequence(
+			"ntazzewyvv",
+			"CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD"
+					+ "EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG"
+					+ "EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW"
+					+ " RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    "
+					+ "W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   "
+					+ "FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI");
+	static FastaSequence s3 = new FastaSequence(" 12 d t y wi 		k	jbke  	",
+			"  KLSHHDCD" + "   N" + "    H" + "    HSKCTEPHCGNSHQML\n\rHRDP"
+					+ "    CCDQCQSWEAENWCASMRKAILF");
+	@Test()
+	public void test() {
+
+		List<FastaSequence> old_seqs = null;
+		final List<FastaSequence> list = new ArrayList<FastaSequence>();
+		try {
+			old_seqs = SequenceUtil.readFasta(new FileInputStream(
+					AllTestSuit.TEST_DATA_PATH + "complicated.fasta"));
+			final FastaReader fr = new FastaReader(AllTestSuit.TEST_DATA_PATH
+					+ "complicated.fasta");
+
+			while (fr.hasNext()) {
+				final FastaSequence fs = fr.next();
+				list.add(fs);
+			}
+		} catch (final FileNotFoundException e) {
+			e.printStackTrace();
+			Assert.fail(e.getLocalizedMessage());
+		} catch (final IOException e) {
+			e.printStackTrace();
+			Assert.fail(e.getLocalizedMessage());
+		}
+		System.out.println("OLD: " + old_seqs);
+		System.out.println("NEW: " + list);
+		Assert.assertEquals(old_seqs.size() + 1, list.size());
+		Assert.assertEquals(old_seqs.get(0), list.get(0));
+		Assert.assertEquals(old_seqs.get(1), list.get(1));
+		// Assert.assertEquals(old_seqs.get(2), list.get(2));
+		// Assert.assertEquals(seqs.get(3), list.get(3));
+
+		Assert.assertEquals(FastaReaderTester.s0, list.get(0));
+		Assert.assertEquals(FastaReaderTester.s1, list.get(1));
+		Assert.assertEquals(FastaReaderTester.s2, list.get(2));
+		Assert.assertEquals(FastaReaderTester.s3, list.get(3));
+
+	}
+}
diff --git a/testsrc/testdata/complicated.fasta b/testsrc/testdata/complicated.fasta
new file mode 100644
index 0000000..3c891d6
--- /dev/null
+++ b/testsrc/testdata/complicated.fasta
@@ -0,0 +1,23 @@
+>zedpshvyzg
+GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
+
+>xovkactesa
+CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
+FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
+FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
+DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
+
+>ntazzewyvv
+CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
+EASINM	AQQWRSLPPSRIMKLNG	HGCDCMHSHMEAD	DTKQSGIKGTFWNG	HDAQWLCRWG	
+EFITEA	WWGRWGAITFFHAH	ENKNEIQECSDQNLKE	SRTTCEIID   TCHLFTRHLDGW 
+  RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
+  W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
+  FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
+
+   > 12 d t y wi 		k	jbke  	
+  KLSHHDCD
+   N
+    H
+    HSKCTEPHCGNSHQMLHRDP
+    CCDQCQSWEAENWCASMRKAILF
\ No newline at end of file