Remove some print commands

Author: cmdcolin

src/perl5/Bio/JBrowse/Cmd/IndexNames.pm

@@ -18,7 +18,6 @@ use Storable ();
 use File::Path ();
 use File::Temp ();
 use List::Util ();
-use Data::Dumper;
 use Encode qw(decode encode);
 
 use GenomeDB ();
@@ -80,7 +79,6 @@ sub run {
     unless( @$refSeqs ) {
         die "No reference sequences defined in configuration, nothing to do.\n";
     }
-    print Dumper($gdb->trackList);
     my @tracks = grep $self->track_is_included( $_->{label} ),
                       @{ $gdb->trackList || [] };
     unless( @tracks ) {
@@ -367,7 +365,6 @@ sub find_names_files {
             # read either names.txt or names.json files
             my $name_records_iterator;
             my $names_txt  = File::Spec->catfile( $dir, 'names.txt'  );
-            print "$names_txt\n";
             if( -e decode('UTF-8',$names_txt) ) {
                 push @files, $self->make_file_record( $track, $names_txt );
             }

src/perl5/Bio/JBrowse/FeatureStream/Genbank.pm

@@ -10,7 +10,6 @@ use strict;
 use warnings;
 
 use base 'Bio::JBrowse::FeatureStream';
-use Data::Dumper;
 
 use Bio::JBrowse::FeatureStream::Genbank::LocationParser;
 
@@ -32,12 +31,11 @@ sub _aggregate_features_from_gbk_record {
     # get index of top level feature ('mRNA' at current writing)
     my $indexTopLevel;
     my $count = 0;
-    print Dumper $record;
     foreach my $feat ( @{$record->{FEATURES}} ){
-        if ( _isTopLevel( $feat ) ){
-            $indexTopLevel = $count;
-        }
-        $count++;
+	if ( _isTopLevel( $feat ) ){
+	    $indexTopLevel = $count;
+	}
+	$count++;
     }
 
     return unless defined $indexTopLevel;
@@ -56,52 +54,55 @@ sub _aggregate_features_from_gbk_record {
     delete $f->{SEQUENCE};
 
     $f->{end} = $locations[-1]{end};
-    $f->{type}   = $record->{FEATURES}[$indexTopLevel]{name};
-    $f->{seq_id} ||= $seq_id;
-
-    %$f = ( %{$record->{FEATURES}[$indexTopLevel]{feature} || {}}, %$f ); # get other attrs
-    if( $f->{type} eq 'gene' ) {
-        print "here2\n";
-        $f->{name} = $record->{FEATURES}[$indexTopLevel]{feature}{gene};
-        $f->{description} = $record->{FEATURES}[$indexTopLevel]{feature}{product} || $f->{FEATURES}[$indexTopLevel]{feature}{note};
-    }
+    #for my $f ( @features ) {
+        $f->{start}  += $offset + 1;
+        $f->{end}    += $offset;
+        $f->{strand} = 1 unless defined $f->{strand};
+        $f->{type}   = $record->{FEATURES}[$indexTopLevel]{name};
+        $f->{seq_id} ||= $seq_id;
+
+        %$f = ( %{$record->{FEATURES}[$indexTopLevel]{feature} || {}}, %$f ); # get other attrs
+        if( $f->{type} eq 'mRNA' ) {
+            $f->{name} = $record->{FEATURES}[$indexTopLevel]{feature}{gene};
+            $f->{description} = $record->{FEATURES}[$indexTopLevel]{feature}{product} || $f->{FEATURES}[$indexTopLevel]{feature}{note};
+        }
 
-    # convert FEATURES to subfeatures
-    $f->{subfeatures} = [];
-    if ( scalar( @{$record->{FEATURES} || [] }) > $indexTopLevel ) {
-        for my $i ( $indexTopLevel + 1 .. $#{$record->{FEATURES}} ) {
-            my $feature = $record->{FEATURES}[$i];
-            my @sublocations = _parseLocation( $feature->{location} );
-            for my $subloc ( @sublocations ) {
-                $subloc->{start} += $offset + 1;
-                $subloc->{end} += $offset;
-
-                my $newFeature = {
-                    %{ $feature->{feature}||{} },
-                    %$subloc,
-                    type  => $feature->{name}
-                    };
-
-                $newFeature->{seq_id} ||= $seq_id;
-
-                push @{$f->{subfeatures}}, $newFeature;
+        # convert FEATURES to subfeatures
+        $f->{subfeatures} = [];
+        if ( scalar( @{$record->{FEATURES} || [] }) > $indexTopLevel ) {
+            for my $i ( $indexTopLevel + 1 .. $#{$record->{FEATURES}} ) {
+                my $feature = $record->{FEATURES}[$i];
+                my @sublocations = _parseLocation( $feature->{location} );
+                for my $subloc ( @sublocations ) {
+                    $subloc->{start} += $offset + 1;
+                    $subloc->{end} += $offset;
+
+                    my $newFeature = {
+                        %{ $feature->{feature}||{} },
+                        %$subloc,
+                        type  => $feature->{name}
+                        };
+
+                    $newFeature->{seq_id} ||= $seq_id;
+
+                    push @{$f->{subfeatures}}, $newFeature;
+                }
             }
         }
-    }
+#    }
 
     return $f;
 }
 
 sub _isTopLevel {
     my $feat = shift;
-    my @topLevelFeatures = qw( gene ); # add more as needed?
+    my @topLevelFeatures = qw( mRNA ); # add more as needed?
     my $isTopLevel = 0;
     foreach my $thisTopFeat ( @topLevelFeatures ){
-        if ( $feat->{'name'} =~ m/$thisTopFeat/ ){
-            print "here\n";
-            $isTopLevel = 1;
-            last;
-        }
+	if ( $feat->{'name'} =~ m/$thisTopFeat/ ){
+	    $isTopLevel = 1;
+	    last;
+	}
     }
     return $isTopLevel;
 }
@@ -114,7 +115,7 @@ sub _getRegionOffset {
 
     my $f = shift;
     my $offset = 0;
-    if ( grep {$_ =~ /REGION\:/} @{$f->{'VERSION'}} ){ # this is a region file
+    if ( grep {$_ =~ /REGION\:/} @{$f->{'VERSION'}} ){ # this is a region file 
  	# get array item after REGION token
  	my $count = 0;
 	my $regionIndexInArray;