[Bioperl-l] Downloading a sequence in genbank format - related problem

Barry Moore barry.moore at genetics.utah.edu
Thu May 17 18:19:46 UTC 2007


Look at the bioperl documentation - there you will find a HowTo on  
SeqIO.  This will help you learn how to write scripts to load genbank  
flat files and you can then iterate over those files and check the  
organism to see if it's one that you want.  You should be able to  
find everything that you need in the documentation.


On May 17, 2007, at 12:14 PM, Diogo Tschoeke wrote:

> Hi Barry thank's for all your help,
> I choose download the Invertebrates division of NCBI to machine...
> but the I don't have thus script to get the sequences of the local  
> file and I know how to write...
> i tried choose change in the script
> the -db => 'nucleotide' for -db => 'local-gbdi.gb'
> like I wrote below
> my $query = Bio::DB::Query::GenBank->new
>                                 (-query   =>'Leishmania major',
>                                 -db     => '>local-gbdi.gb );
> my $gb = new Bio::DB::GenBank;
> my $seqio = $gb->get_Stream_by_query($query);
> but didn't work because de Bio:DB::Query::GenBank is a perl module  
> wich conect at Ncbi to do my query and my Database is now local.
>  I need the genomes of Trypanosoma cruzi, Trypanosoma brucei,  
> Leishmania major, Entamoeba and Plasmodium falciparum in the  
> genbank format file.
> Any Sugestion? Somebody have this script?
> Help!
> And thank's for the help!
> Diogo Tschoeke
> Laboratory of Molecular Biology of Trypanosomatides
> Fundação Osvaldo Cruz - Fiocruz RJ, Brazil
> http://biowebdb.org

More information about the Bioperl-l mailing list