Ap11-219, AP11-220

IntersectAustralia · Jun 26, 2013 · ad7b5e0 · ad7b5e0
1 parent 743faf4
commit ad7b5e0
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Showing 15 changed files with 12,389 additions and 12,371 deletions.
diff --git a/dist/codon_finder.jar b/dist/codon_finder.jar
diff --git a/dist/nucleotide_to_amino_acid.jar b/dist/nucleotide_to_amino_acid.jar
diff --git a/dist/protein_generator.jar b/dist/protein_generator.jar
diff --git a/dist/results_analyser.jar b/dist/results_analyser.jar
diff --git a/dist/samifier.jar b/dist/samifier.jar
diff --git a/dist/virtual_protein_merger.jar b/dist/virtual_protein_merger.jar
diff --git a/src/au/org/intersect/samifier/Version.java b/src/au/org/intersect/samifier/Version.java
@@ -2,5 +2,5 @@
 
 public interface Version {
 
-    String VERSION = "1.0.7";
+    String VERSION = "1.0.8";
 }
diff --git a/src/au/org/intersect/samifier/domain/GffOutputter.java b/src/au/org/intersect/samifier/domain/GffOutputter.java
@@ -12,6 +12,7 @@ public class GffOutputter implements Outputter {
     private String directionFlag;
     private String glimmerName;
     private Set<String> virtualProteinNames;
+    private String origin;
 
     public GffOutputter(ProteinLocation location,
             String genomeFileNameWithExtension) {
@@ -26,6 +27,7 @@ public GffOutputter(ProteinLocation location,
         this.directionFlag = location.getDirection();
         this.glimmerName = location.getName();
         this.virtualProteinNames = location.getVirtualProteinNames();
+        this.origin = location.getOrigin();
     }
 
     @Override
@@ -45,7 +47,11 @@ public String getOutput() {
     private String getOutputLine(String type, boolean addParent) {
         StringBuilder output = new StringBuilder();
         output.append(genomeFileName);
-        column(output, "Glimmer");
+        if (origin != null && origin.length() >0 ) {
+            column(output, origin);
+        } else {
+            column(output, "Glimmer");
+        }
         column(output, type);
         column(output, Integer.toString(start));
         column(output, Integer.toString(end));

diff --git a/src/au/org/intersect/samifier/domain/ProteinLocation.java b/src/au/org/intersect/samifier/domain/ProteinLocation.java
@@ -15,8 +15,9 @@ public class ProteinLocation implements Comparable<ProteinLocation> {
 
     private String frame;
     private String peptideAbsoluteStartStop;
-
+    
     private Set<String> virtualProteinNames;
+    private String origin;
 
     public ProteinLocation(String name, int startIndex, int length,
             String direction, String frame) {
@@ -128,4 +129,12 @@ public String getAbsoluteStartStop() {
         return peptideAbsoluteStartStop;
     }
 
+    public String getOrigin() {
+        return origin;
+    }
+
+    public void setOrigin(String origin) {
+        this.origin = origin;
+    }
+
 }
diff --git a/src/au/org/intersect/samifier/generator/CodonsPerIntervalLocationGenerator.java b/src/au/org/intersect/samifier/generator/CodonsPerIntervalLocationGenerator.java
@@ -116,9 +116,11 @@ private void addLocations(List<ProteinLocation> locations, int start,
                     + (isForward ? "+" : "-") + (subIndex + 1);
             int length = endIndex - startIndex + 1;
             String frame = Integer.toString(subIndex + 1);
-            locations.add(new ProteinLocation(name, startIndex, length,
+            ProteinLocation location = new ProteinLocation(name, startIndex, length,
                     isForward ? GenomeConstant.FORWARD_FLAG
-                            : GenomeConstant.REVERSE_FLAG, frame, null, null, chromosome));
+                            : GenomeConstant.REVERSE_FLAG, frame, null, null, chromosome);
+            location.setOrigin("VPGenerator");
+            locations.add(location);
         }
     }
 

diff --git a/src/au/org/intersect/samifier/generator/VirtualProteinMascotLocationGenerator.java b/src/au/org/intersect/samifier/generator/VirtualProteinMascotLocationGenerator.java
@@ -168,6 +168,7 @@ public List<ProteinLocation> doGenerateLocations()
                     geneInfo.getDirectionStr(), "0", peptideSearchResult.getConfidenceScore(),
                     peptideSearchResult.getProteinName() + "(" + (virtualGeneStart + 1) + "-" + (virtualGeneStop + 1) + ")", geneInfo.getChromosome());
             loc.setAbsoluteStartStop(getStartPosition(startPosition, stopPosition) + "_" + Math.abs(stopOffset - startOffset));
+            loc.setOrigin("VPMerger");
             proteinLocations.add(loc);
         }
         return proteinLocations;

diff --git a/src/au/org/intersect/samifier/runner/SamifierRunner.java b/src/au/org/intersect/samifier/runner/SamifierRunner.java
@@ -208,7 +208,7 @@ public void createSAM(List<PeptideSearchResult> peptideSearchResults,
         }
         output.write("@HD\tVN:1.0\n");
         for (String chromosome : chromosomes) {
-            output.write("@SQ\tSN:" + chromosome + "\tLN:" + ((sequenceGenerator.getFastaParser().getChromosomeLength(chromosome)) / 3)  + "\n");
+            output.write("@SQ\tSN:" + chromosome + "\tLN:" + ((sequenceGenerator.getFastaParser().getChromosomeLength(chromosome)))  + "\n");
         }
 
         for (SAMEntry samEntry : samEntries) {

diff --git a/test/resources/expected.sam b/test/resources/expected.sam
@@ -1,7 +1,7 @@
 @HD	VN:1.0
-@SQ	SN:chrI	LN:76739
-@SQ	SN:chrIV	LN:510644
-@SQ	SN:chrXVI	LN:344654
+@SQ	SN:chrI	LN:230218
+@SQ	SN:chrIV	LN:1531933
+@SQ	SN:chrXVI	LN:1033964
 KPYK1_YEAST.q131_p1	0	chrI	71969	40	21M	=	0	0	TCTGTCATTGACAACGCCAGA	*
 KPYK1_YEAST.q217_p1	0	chrI	73163	37	21M	*	0	0	ATCAACTTCGGTATTGAAAAG	*
 KPYK1_YEAST.q21_p1	0	chrI	73190	25	18M	*	0	0	GAATTCGGTATCTTGAAG	*

diff --git a/test/resources/expected_filtered.sam b/test/resources/expected_filtered.sam
@@ -1,6 +1,6 @@
 @HD	VN:1.0
-@SQ	SN:chrI	LN:76739
-@SQ	SN:chrIV	LN:510644
+@SQ	SN:chrI	LN:230218
+@SQ	SN:chrIV	LN:1531933
 KPYK1_YEAST.q131_p1	0	chrI	71969	40	21M	=	0	0	TCTGTCATTGACAACGCCAGA	*
 KPYK1_YEAST.q217_p1	0	chrI	73163	37	21M	*	0	0	ATCAACTTCGGTATTGAAAAG	*
 RL31A_YEAST.q1009_p2	0	chrIV	322256	52	27M	=	0	0	GAATACACCATTAACTTGCACAAAAGA	*