[Bioperl-l] Downloading a sequence in genbank format - related problem
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?
> And thank's for the help!
> Diogo Tschoeke
> Laboratory of Molecular Biology of Trypanosomatides
> Fundação Osvaldo Cruz - Fiocruz RJ, Brazil
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