add bed parser

lib/Tests/PassParser.pm

@@ -8,6 +8,7 @@ use Benchmark;
 
 use lib "$FindBin::Bin/lib";
 use Record::Pass;
+use Record::Bed;
 
 # constructor
 sub new
@@ -65,38 +66,101 @@ sub parse
 {
     my $self = shift;
     my $count = 0;
+    my $total = 0;
+    my $notail = 0;
+    my $mito = 0;
+    my $window_upstream = 20000;
+    my %featureScores = (
+        'notail' => 11,
+        'mitochondria' => 9,
+        'intergenic' => 10,
+        '5pUTR_extended' => 8,
+        '5pUTR_intron' => 7,
+        '5pUTR' => 6,
+        'CDS' => 5,
+        'intron' => 4,
+        '3pUTR' => 1,
+        '3pUTR_intron' => 3,
+        '3pUTR_extended' => 2,
+    );
+
 
     my $t0 = Benchmark->new();
 
+    my %stats = ();
+
     while(my $line = $self->read())
     {
         chomp($line);
+        $count++;
 
         # create pass object
         my $pass = Pass->new($line);
 
         # count no tail
+        $stats{'pass'}{'total'}++;
+        $stats{'reads'}{'total'} += $pass->{readsSumCoverage};
+
+        # allocate counters
+        my $feature = 'intergenic';
+
+
         if ($pass->ispoly() == 0)
         {
-            $notail += $pass->{readsSumCoverage};
+            $feature = 'notail';
         }
         elsif ($pass->ischrom('chrM'))
         {
-            $mito += $pass->{readsSumCoverage};
+            $feature = 'mito';
+        }
+        else
+        {
+            my $iter = $self->{annotation}->query($pass->region($window_upstream));
+            my $prevFeatureScore = $featureScores{'notail'};
+            my $hits = 0;
+
+            while (my $line = $iter->next)
+            {
+                # current bed record
+                my $bed = Bed->new($line);
+
+                # skip different strand
+                next if($bed->{strand} ne $pass->{strand});
+
+                # process bed hit
+                (my $tmp, $feature) = $bed->closest($pass->{tailsBestBase});
+
+                # increment hits
+                $hits++;
+
+                # get scores
+                my $currFeatureScore = $featureScores{$feature};
+                print $pass->{name},"\t",$bed->{name},"\t",$feature,"\t",$currFeatureScore,"\n";
+
+                # update score
+                $prevFeatureScore = $currFeatureScore;
+
+            }
+
+            last if($hits > 1);
+
         }
 
-
-        print $pass->{name},"\n";
-        last;
+        $stats{'reads'}{$feature} += $pass->{readsSumCoverage};
+        $stats{'pass'}{$feature}++;
 
 
-        $count++;
     }
     my $t1 = Benchmark->new();
     my $td = timediff($t1, $t0);
-    print "benchmark :: ",timestr($td),"\n";
-    print $count,"\n";
-
+    print "# benchmark :: ",timestr($td),"\n";
+=head
+    print "# feature\tpass\treads\n";
+    foreach my $key (sort keys %{$stats{'reads'}})
+    {
+        print $key,"\t",$stats{'pass'}{$key},"\t",sprintf("%.2f",100*$stats{'pass'}{$key}/$stats{'pass'}{'total'}),"\t",$stats{'reads'}{$key},"\t",sprintf("%.2f",100*$stats{'reads'}{$key}/$stats{'reads'}{"total"}),"\n";
+    }
+=cut
 }
 
 1; # return true value