[Bioperl-guts-l] [14443] bioperl-live/trunk/Bio/FeatureIO/bed.pm: improved handling of different kinds of feature object

Senduran Balasubramaniam sendu at dev.open-bio.org
Wed Jan 16 05:54:01 EST 2008


Revision: 14443
Author:   sendu
Date:     2008-01-16 05:54:01 -0500 (Wed, 16 Jan 2008)

Log Message:
-----------
improved handling of different kinds of feature object

Modified Paths:
--------------
    bioperl-live/trunk/Bio/FeatureIO/bed.pm

Modified: bioperl-live/trunk/Bio/FeatureIO/bed.pm
===================================================================
--- bioperl-live/trunk/Bio/FeatureIO/bed.pm	2008-01-16 10:51:53 UTC (rev 14442)
+++ bioperl-live/trunk/Bio/FeatureIO/bed.pm	2008-01-16 10:54:01 UTC (rev 14443)
@@ -184,6 +184,13 @@
   } else {
     $name = 'anonymous';
   }
+  
+  if (ref($name)) {
+    $name = $name->value;
+  }
+  if (ref($chrom)) {
+    $chrom = $chrom->value;
+  }
 
   my $score = $feature->score || 0;
   my $strand = $feature->strand == 0 ? '-' : '+'; #default to +
@@ -194,7 +201,7 @@
   my $block_sizes = '';  #not implemented, used for sub features
   my $block_starts = ''; #not implemented, used for sub features
 
-  $self->_print(join("\t",($chrom->value,$chrom_start,$chrom_end,$name->value,$score,$strand,$thick_start,$thick_end,$reserved,$block_count,$block_sizes, $block_starts))."\n");
+  $self->_print(join("\t",($chrom,$chrom_start,$chrom_end,$name,$score,$strand,$thick_start,$thick_end,$reserved,$block_count,$block_sizes, $block_starts))."\n");
   $self->write_feature($_) foreach $feature->get_SeqFeatures();
 }
 




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