[Bioperl-l] Downloading a sequence in genbank format

[Diogo Tschoeke]

Thank for your help Barry!!

It`s work very fine and i`'m using the script... like you said...
The error was on the print that`s right?
I need to use a while to print all sequeces...

Thanks a Lot

Diogo Tschoeke
Laboratory of Molecular Biology of Trypanosomatides
Fundação Osvaldo Cruz - Fiocruz RJ, Brazil
http://biowebdb.org

2007/5/15, Barry Moore <barry.moore at genetics.utah.edu>:
>
> Diogo-
>
> write_seq expects to be given a Bio::Seq object, not a Bio::SeqIO
> object.  Try this
>
> use strict;
> use warnings;
>
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GenBank;
>
> my $query = Bio::DB::Query::GenBank->new
>                                  (-query   =>'Leishmania major
> [Organism]',
>                                   -db      => 'nucleotide');
> my $gb = new Bio::DB::GenBank;
> my $seqio = $gb->get_Stream_by_query($query);
>
> my $out = Bio::SeqIO->new(-format => 'genbank',
>                            -file => '>>teste6.gb');
> while (my $seq = $seqio->next_seq) {
>          $out->write_seq($seq);
> }
>
> Barry
>
> On May 15, 2007, at 4:44 PM, Diogo Tschoeke wrote:
>
> > Dear All,
> >
> > I need to download a lot of sequence of Leishmania major in genbank
> > format...
> > But i can't download on the page of NCBI, because the downloaded
> > file are
> > corrupted... when i use a browser to download this sequences
> > And them i looking for some script to download that`s file and fink
> > something like that:
> >
> >
> > #########################################################
> > use strict;
> > use warnings;
> >
> > use Bio::Seq;
> > use Bio::SeqIO;
> > use Bio::DB::GenBank;
> >
> > my $query = Bio::DB::Query::GenBank->new
> >                                 (-query   =>'Leishmania major
> > [Organism]',
> >                                 -db      => 'nucleotide');
> > my $gb = new Bio::DB::GenBank;
> > my $seqio = $gb->get_Stream_by_query($query);
> >
> > my $out = Bio::SeqIO->new(-format => 'genbank',
> >                           -file => '>>teste6.gb');
> > $out->write_seq($seqio);
> > #########################################################
> >
> > And the system return me this erros
> > [diogo1 at genome perl]$ perl teste6.pl
> >
> > -------------------- WARNING ---------------------
> > MSG:  Bio::SeqIO::genbank=HASH(0x96c0f08) is not a SeqI compliant
> > module.
> > Attempting to dump, but may fail!
> > ---------------------------------------------------
> > Can't locate object method "seq" via package "Bio::SeqIO::genbank" at
> > /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 692.
> >
> > Any Ideia?
> >
> > Thank`s
> >
> > Diogo Tschoeke
> > Laboratory of Molecular Biology of Trypanosomatides
> > Fundação Osvaldo Cruz - Fiocruz RJ, Brazil
> > http://biowebdb.org
> >
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>
>