[Bioperl-l] bond() FT operator

Aaron J Mackey Aaron J. Mackey" <amackey@virginia.edu
Mon Jan 20 15:44:31 EST 2003

Looks like there's a new feature table operator in town: bond()

Try this on for size:
perl -MBio::DB::GenPept -e '$d = new Bio::DB::GenPept; $s = $db->get_Seq_by_id("230350");'

Here's what we did to fix it locally, but someone with more emotional
investment in FTLocationFactory should decide the "right thing to do";
this fix just loses the Bond features entirely (or any other new feature
type operation that NCBI may spring on us) ...


Index: Bio/Factory/FTLocationFactory.pm
RCS file:
retrieving revision 1.9
diff -r1.9 FTLocationFactory.pm
<           $self->throw("operator \"$op\" unrecognized by parser");
>           $self->warn("operator \"$op\" unrecognized by parser");

Index: Bio/SeqIO/genbank.pm
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/genbank.pm,v
retrieving revision 1.77
diff -r1.77 genbank.pm
<             if($species && ($feat->primary_tag eq 'source') &&
>             if($species && $feat && ($feat->primary_tag eq 'source') &&
<             push(@features, $feat);
>             push(@features, $feat) if $feat;

 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821

More information about the Bioperl-l mailing list