Merge pull request #24 from carandraug/bp_genbank_ref_extractor

genbank_ref_extractor
bioperl · Sep 22, 2011 · 2740991 · 2740991
2 parents 8f9089f + 77c7e35
commit 2740991
Showing 1 changed file with 9 additions and 6 deletions.
diff --git a/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl b/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl
@@ -57,7 +57,7 @@ =head1 OPTIONS
 is a regex that will case-insensitive. If it matches more than one assembly, it will
 use the first match. It defauls to C<reference (primary )?assembly>.
 =cut
-my $assemly_regex = 'reference (primary )?assembly';
+my $assembly_regex = 'reference (primary )?assembly';
 
 =item B<--debug>
 
@@ -293,7 +293,7 @@ =head1 NOTES ON USAGE
 ################################################################################
 
 GetOptions(
-            'assembly:s'          => \$assemly_regex,
+            'assembly:s'          => \$assembly_regex,
             'debug'               => \$debug,
             'down|downstream=i'   => \$downstream,
             'format=s'            => \$format,
@@ -534,7 +534,7 @@ sub analyze_entrez_genes {
 
     foreach my $l (@{$result->{'locus'}}){
       $l = $l->[0] if(ref($l) eq 'ARRAY');
-      next unless ($l->{'heading'} && $l->{'heading'} =~ m/$assemly_regex/i);
+      next unless ($l->{'heading'} && $l->{'heading'} =~ m/$assembly_regex/i);
       my $ChrAccVer = $l->{'accession'};
       my $ChrStart  = $l->{'seqs'}->[0]->{'int'}->[0]->{'from'};
       my $ChrStop   = $l->{'seqs'}->[0]->{'int'}->[0]->{'to'};
@@ -815,11 +815,8 @@ sub get_time {
 characters are allowed. All other characters will be replaced by an underscore. Allowed characters
 are:
 
-=over
-
 B<a-z 0-9 - +  . , () {} []'>
 
-=back
 =cut
 
 ## Tries to sanitize a filename
@@ -1062,3 +1059,9 @@ sub get_product_list {
     default    { return map { $self->get_product_list($product, $_) } @_; }
   }
 }
+
+## this =back closes the last point on the NOTES on usage section
+
+=back
+
+=cut