[Bioperl-l] GI identifier missing when using Bio::Index::GenBank?
osborne1 at optonline.net
Thu Apr 27 12:29:43 EDT 2006
Can't you go directly from the daily update to the database?
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');
> Diffing to the original GenBank record, the only difference is the GI
> diff CJ521890_orig.out CJ521890_seqio.out
> < 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
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l