[Bioperl-l] bond() FT operator

[Aaron J Mackey]

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) ...

-Aaron

Index: Bio/Factory/FTLocationFactory.pm
===================================================================
RCS file:
/home/repository/bioperl/bioperl-live/Bio/Factory/FTLocationFactory.pm,v
retrieving revision 1.9
diff -r1.9 FTLocationFactory.pm
160c160
<           $self->throw("operator \"$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
386c386
<             if($species && ($feat->primary_tag eq 'source') &&
---
>             if($species && $feat && ($feat->primary_tag eq 'source') &&
395c395
<             push(@features, $feat);
---
>             push(@features, $feat) if $feat;


-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu