(I had sent this yesterday but it failed. Apologies if you receive
multiple copies.)
Hm. I will check this. If you have got a minute and want to do me a
favor :) can you submit it as a bug report?
Is the same insane idea (folding location and feature key together)
behind this operator as with the once dreaded and then (fortunately)
abandoned replace()?
-hilmar
On Monday, January 20, 2003, at 07:44 AM, Aaron J Mackey wrote:
>
> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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