[Bioperl-l] GI identifier missing when using Bio::Index::GenBank?

Brian Osborne osborne1 at optonline.net
Thu Apr 27 12:29:43 EDT 2006


Todd,

Can't you go directly from the daily update to the database?

Brian O.


On 4/26/06 9:47 PM, "Todd Richmond" <richmond.todd at gmail.com> wrote:

> I've got an application where I grab the daily updates from NCBI, pull
> out just the plant sequences and store them in a separate flat file.
> Then I use Bio::Index::GenBank to index the plant flat file so I can
> pull out my sequences of interest. I'm in the midst of converting my
> scripts to using bioperl-db/biosql so I can push those sequences into
> the database. The problem is that the NCBI GI identifier isn't
> returned when using the index file.
> 
> When I run the following test script:
> ***
> use Bio::Index::GenBank;
> use Bio::SeqIO;
> use strict;
> my $Index_File_Name = 'nc0425.idx';
> my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_Name);
> 
> my $seqio = new Bio::SeqIO( '-format' => 'genbank' );
> my $seq = $inx->get_Seq_by_acc('CJ521890');
> $seqio->write_seq($seq);
> ***
> 
> Diffing to the original GenBank record, the only difference is the GI
> identifier:
> 
> diff CJ521890_orig.out CJ521890_seqio.out
> 5c5
> < VERSION     CJ521890.1  GI:93266243
> ---
>> VERSION     CJ521890.1
> 
> Is this expected behaviour? If so, is there a workaround that will
> allow me to retrieve the GI from the index file so I can store it in
> the bioentry table?
> 
> Thanks, Todd
> 
> 
> --
> Todd Richmond
> richmond.todd at gmail.com
> 
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