exon_count.pl

pedros · Feb 8, 2011 · 1ee2fdb · 1ee2fdb
1 parent ae11147
commit 1ee2fdb
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/GFF/lib/GFF/Parser.pm b/GFF/lib/GFF/Parser.pm
@@ -119,7 +119,7 @@ sub slurp_index{
             $counter++;
         }
     }
-    carp "warning: $badrecords out of $counter records didn't have a column/attribute $column in $self->file_or_handle"
+    carp "warning: $badrecords out of $counter records didn't have a column/attribute $column in " . $self->file_or_handle
     if $badrecords;
 
     return \%index;
@@ -183,7 +183,8 @@ sub _parse_gff_hashref{
     }
 
     if ($locus_tag){
-        if ($accum{$locus_tag} =~ /([^\.]+)\.([^\.]+)/){
+        if (exists($accum{$locus_tag}) && 
+            $accum{$locus_tag} =~ /([^\.]+)\.([^\.]+)/){
             $accum{$locus_tag . '.prefix'} = $1;
             $accum{$locus_tag . '.suffix'} = $2;
         } else {

diff --git a/exon_filter.pl b/exon_filter.pl
@@ -9,8 +9,8 @@
 use Pod::Usage;
 use Getopt::Long;
 use FindBin;
-use lib "$FindBin::Bin/DZLab-Tools/lib";
-use DZLab::Tools::GFF qw/gff_to_string gff_slurp/;
+use lib "$FindBin::Bin/GFF/lib";
+use GFF;
 
 my $locus_tag = q/ID/;
 my $input;