add tree in constructor

MPIBR-Bioinformatics · May 20, 2017 · 48f388f · 48f388f
1 parent fab7e90
commit 48f388f
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Showing 6 changed files with 47 additions and 23 deletions.
diff --git a/PASSAnnotator.pl b/PASSAnnotator.pl
@@ -24,8 +24,8 @@
 
 
 
-# my $obj = BedParser->new($queryFile);
-# $obj->parse();
+#my $obj = BedParser->new($queryBedFile);
+#$obj->parse();
 
 
 my $obj = PassParser->new($queryPassFile, $queryBedFile);

diff --git a/PASSAnnotator.xcodeproj/project.pbxproj b/PASSAnnotator.xcodeproj/project.pbxproj
@@ -11,7 +11,6 @@
 		B179B9361EC676A1006FA542 /* PASSAnnotator.pl */ = {isa = PBXFileReference; lastKnownFileType = text.script.perl; path = PASSAnnotator.pl; sourceTree = "<group>"; };
 		B1BE38C01ECDA7FF0017F94D /* Bed.pm */ = {isa = PBXFileReference; lastKnownFileType = text.script.perl; name = Bed.pm; path = lib/Record/Bed.pm; sourceTree = "<group>"; };
 		B1BE38C11ECDA7FF0017F94D /* Pass.pm */ = {isa = PBXFileReference; lastKnownFileType = text.script.perl; name = Pass.pm; path = lib/Record/Pass.pm; sourceTree = "<group>"; };
-		B1BE38C71ECDC2B20017F94D /* BedTree.pm */ = {isa = PBXFileReference; lastKnownFileType = text.script.perl; name = BedTree.pm; path = lib/Tests/BedTree.pm; sourceTree = "<group>"; };
 		B1BE38C81ECDC5380017F94D /* BedParser.pm */ = {isa = PBXFileReference; lastKnownFileType = text.script.perl; name = BedParser.pm; path = lib/Tests/BedParser.pm; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
@@ -37,7 +36,6 @@
 		B1BE38C51ECDC20F0017F94D /* Tests */ = {
 			isa = PBXGroup;
 			children = (
-				B1BE38C71ECDC2B20017F94D /* BedTree.pm */,
 				B1BE38C81ECDC5380017F94D /* BedParser.pm */,
 				B16A7F0C1ECF1D9E004F1B12 /* PassParser.pm */,
 			);

diff --git a/lib/Record/Bed.pm b/lib/Record/Bed.pm
@@ -30,10 +30,15 @@ sub new
     $self->{blockStarts} = $bed_vals[11];
     $self->{exons} = ();
     $self->{introns} = ();
+    $self->{tree} = ();
+    $self->{thickStartNode} = ();
+    $self->{thickEndNode} = ();
 
     # assign features
     $self->getExons();
     $self->getIntrons();
+    $self->getFeaturesTree();
+    $self->getTickNodes();
 
 
     return $self;
@@ -129,48 +134,54 @@ sub getIntrons
     $self->{introns} = \@introns;
 }
 
-# BEDTREE
-sub bedTree
+# Red-Black Features Tree
+sub getFeaturesTree
 {
     my $self = shift;
 
     # allocate tree
-    my $btree = Tree::Interval->new();
+    $self->{tree} = Tree::Interval->new();
 
     # insert exons
     my $exons_cnt = scalar(@{$self->{exons}});
     for(my $ex = 0; $ex < $exons_cnt; $ex++)
     {
-        $btree->insert($self->{exons}->[$ex][0], $self->{exons}->[$ex][1], ['exon', $self->{exons}->[$ex][2], $exons_cnt]);
+        $self->{tree}->insert($self->{exons}->[$ex][0], $self->{exons}->[$ex][1], ['exon', $self->{exons}->[$ex][2], $exons_cnt]);
     }
 
     # insert introns
     my $introns_cnt = scalar(@{$self->{introns}});
     for (my $in = 0; $in < $introns_cnt; $in++)
     {
-        $btree->insert($self->{introns}->[$in][0], $self->{introns}->[$in][1], ['intron', $self->{introns}->[$in][2], $introns_cnt]);
+        $self->{tree}->insert($self->{introns}->[$in][0], $self->{introns}->[$in][1], ['intron', $self->{introns}->[$in][2], $introns_cnt]);
     }
 
-    # return tree reference
-    return $btree;
 }
 
+# Nodes for thicks Start and End
+sub getTickNodes
+{
+    my $self = shift;
+
+    $self->{thickStartNode} = $self->{tree}->find($self->{thickStart});
+    $self->{thickEndNode} = $self->{tree}->find($self->{thickEnd});
+
+}
+
+
 sub closest
 {
     my $self = shift;
     my $base = shift;
 
-    # generate bed tree
-    my $btree = $self->bedTree();
-
     # check base
-    my $hitBase = $btree->find($base);
+    my $baseNode = $self->{tree}->find($base);
 
     # allocate feature
     my $feature = '<unknown>';
 
     # root condition
-    my $cond_hit = defined($hitBase) ? $hitBase->[0] : 'intergenic';
+    my $cond_hit = defined($baseNode) ? $baseNode->[0] : 'intergenic';
 
     # decision tree
     if ($cond_hit eq 'exon')
@@ -197,11 +208,9 @@ sub closest
         $feature =~ tr/53/35/;
     }
 
-    return ($hitBase, $feature);
+    return ($baseNode, $feature);
 }
 
 
 
-
-
 1; # return true
diff --git a/lib/Record/Pass.pm b/lib/Record/Pass.pm
@@ -52,7 +52,7 @@ sub ischrom
     return $ischrom;
 }
 
-sub region
+sub window
 {
     my $self = shift;
     my $window_upstream = shift;
@@ -75,4 +75,13 @@ sub region
     return $self->{chrom} . ":" . $queryLeft . "-" . $queryRight;
 }
 
+sub regions
+{
+    my $self = shift;
+    my $bed = shift;
+    my $baseNode = shift;
+    my $feature = shift;
+
+}
+
 1; # return true
diff --git a/lib/Tests/BedParser.pm b/lib/Tests/BedParser.pm
@@ -78,10 +78,13 @@ sub parse
         # process bed hit
         my ($hit, $feature) = $bed->closest($randomBase);
 
-        #print $bed->{name},"\t",$feature,"\n";
+        # pass regions
+
+        print $bed->{name},"\t",$feature,"\t",$bed->{thickEndNode}[0],"\n";
 
 
         $count++;
+        last if($count == 100);
     }
     my $t1 = Benchmark->new();
     my $td = timediff($t1, $t0);

diff --git a/lib/Tests/PassParser.pm b/lib/Tests/PassParser.pm
@@ -115,7 +115,7 @@ sub parse
         }
         else
         {
-            my $iter = $self->{annotation}->query($pass->region($window_upstream));
+            my $iter = $self->{annotation}->query($pass->window($window_upstream));
             my $prevFeatureScore = $featureScores{'notail'};
             my $hits = 0;
 
@@ -128,8 +128,13 @@ sub parse
                 next if($bed->{strand} ne $pass->{strand});
 
                 # process bed hit
-                (my $tmp, $feature) = $bed->closest($pass->{tailsBestBase});
+                (my $bnode, $feature) = $bed->closest($pass->{tailsBestBase});
 
+                # export features
+                $pass->regions($bed, $bnode, $feature);
+
+
+
                 # increment hits
                 $hits++;