GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java

@@ -158,7 +158,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         List<ReferenceOrderedData> rods = new ArrayList<ReferenceOrderedData>();
 
         if (TEST_ROD) {
-            ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class);
+            ReferenceOrderedData gff = new ReferenceOrderedData(new File("single.gff"), rodGFF.class);
             gff.testMe();
 
             //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );

java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.refdata;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.FileNotFoundException;
 import java.util.Iterator;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -10,6 +11,8 @@ import java.util.Collections;
 import edu.mit.broad.picard.util.TabbedTextFileParser;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.Utils;
 
 /**
  * Class for representing arbitrary reference ordered data sets
@@ -38,12 +41,14 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     //
     // ----------------------------------------------------------------------
     public void testMe() {
-        ReferenceOrderedDatum last = null;
         for ( ReferenceOrderedDatum rec : this ) {
-            if ( last == null || ! last.getLocation().onSameContig(rec.getLocation()) ) {
             System.out.println(rec.toString());
+
+            rodGFF gff = (rodGFF)rec;
+            String[] keys = {"LENGTH", "ALT", "FOBARBAR"};
+            for ( String key : keys) {
+                System.out.printf("  -> %s is (%s)%n", key, gff.containsAttribute(key) ? gff.getAttribute(key) : "none");
             }
-            last = rec;
         }
         System.exit(1);
     }
@@ -98,19 +103,25 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     //
     // ----------------------------------------------------------------------
     private class SimpleRODIterator implements Iterator<ROD> {
-        //private WhitespaceTextFileParser parser = null;
+        private xReadLines parser = null;
-        private TabbedTextFileParser parser = null;
 
         public SimpleRODIterator() {
-            parser = new TabbedTextFileParser(true, file);
+            try {
+                parser = new xReadLines(file);
+            } catch ( FileNotFoundException e ) {
+                Utils.scareUser("Couldn't open file: " + file);
+            }
         }
 
         public boolean hasNext() {
+            //System.out.printf("Parser has next: %b%n", parser.hasNext());
             return parser.hasNext();
         }
 
         public ROD next() {
-            String parts[] = parser.next();
+            final String line = parser.next();
+            //System.out.printf("Line is %s%n", line);
+            String parts[] = line.split("\t");
             return parseLine(parts);
         }
  
@@ -119,6 +130,28 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         }
     }
 
+//    private class SimpleRODIterator implements Iterator<ROD> {
+//        //private WhitespaceTextFileParser parser = null;
+//        private TabbedTextFileParser parser = null;
+//
+//        public SimpleRODIterator() {
+//            parser = new TabbedTextFileParser(true, file);
+//        }
+//
+//        public boolean hasNext() {
+//            return parser.hasNext();
+//        }
+//
+//        public ROD next() {
+//            String parts[] = parser.next();
+//            return parseLine(parts);
+//        }
+//
+//        public void remove() {
+//            throw new UnsupportedOperationException();
+//        }
+//    }
+
     public class RODIterator implements Iterator<ROD> {
         private PushbackIterator<ROD> it;
         private ROD prev = null;

java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java

@@ -1,9 +1,14 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import java.util.HashMap;
+import java.util.Scanner;
+import java.util.Map;
+import java.util.regex.MatchResult;
+import java.util.regex.Pattern;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
 
 /**
  * Class for representing arbitrary reference ordered data sets
@@ -75,13 +80,31 @@ public class rodGFF extends ReferenceOrderedDatum {
         return attributes.get(key);
     }
 
+    public boolean containsAttribute(final String key) {
+        return attributes.containsKey(key);
+    }
+
+    public HashMap<String,String> getAttributes() {
+        return attributes;
+    }
+
+    public String getAttributeString() {
+        String[] strings = new String[attributes.size()];
+        int i = 0;
+        for ( Map.Entry<String, String> pair : attributes.entrySet() ) {
+            strings[i++] = pair.getKey() + " " + pair.getValue();
+            //strings[i++] = "(" + pair.getKey() + ") (" + pair.getValue() + ")";
+        }
+        return Utils.join(" ; ", strings);
+    }
+
     // ----------------------------------------------------------------------
     //
     // formatting
     //
     // ----------------------------------------------------------------------
     public String toString() {
-        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s", contig, source, feature, start, stop, score, strand, frame);
+        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop, score, strand, frame, getAttributeString());
     }
 
     public String repl() {
@@ -92,6 +115,25 @@ public class rodGFF extends ReferenceOrderedDatum {
         return String.format("%s", feature);
     }
 
+
+    private static Pattern GFF_DELIM = Pattern.compile("\\s+;\\s*");
+    private static Pattern GFF_ATTRIBUTE_PATTERN = Pattern.compile("([A-Za-z][A-Za-z0-9_]*)((?:\\s+\\S+)+)");
+    final private HashMap<String, String> parseAttributes( final String attributeLine ) {
+        HashMap<String, String> attributes = new HashMap<String, String>();
+        Scanner scanner = new Scanner(attributeLine);
+        scanner.useDelimiter(GFF_DELIM);
+        while ( scanner.hasNext(GFF_ATTRIBUTE_PATTERN) ) {
+            MatchResult result = scanner.match();
+            String key = result.group(1);
+            String value = result.group(2).replace("\"", "").trim();
+            //System.out.printf("  Adding %s / %s (total %d)%n", key, value, result.groupCount());
+            attributes.put(key, value);
+            String n = scanner.next();
+            //System.out.printf("  next is %s%n", n);
+        }
+        return attributes;
+    }
+
     public void parseLine(final String[] parts) {
         //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
 
@@ -107,7 +149,8 @@ public class rodGFF extends ReferenceOrderedDatum {
 
         final String strand = parts[6];
         final String frame = parts[7];
-        HashMap<String, String> attributes = null;
+        final String attributeParts = Utils.join(" ", parts, 8, parts.length);
+        HashMap<String, String> attributes = parseAttributes(attributeParts);
         setValues(contig, source, feature, start, stop, score, strand, frame, attributes);
     }
 }

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -212,11 +212,15 @@ public class Utils {
     }
 
     public static String join(String separator, String[] strings) {
-        if (strings.length == 0) {
+        return join(separator, strings, 0, strings.length);
+    }
+
+    public static String join(String separator, String[] strings, int start, int end) {
+        if ((end - start) == 0) {
             return "";
         }
-        StringBuilder ret = new StringBuilder(strings[0]);
+        StringBuilder ret = new StringBuilder(strings[start]);
-        for (int i = 1; i < strings.length; ++i) {
+        for (int i = start+1; i < end; ++i) {
             ret.append(separator);
             ret.append(strings[i]);
         }