[Bioperl-l] get_Seq_by_id: CONTIG found

[Smithies, Russell]

Hi O'car,

Your code works for me with the proxy stuff (on our proxy) so I suggest
looking there.
Are you using the right proxy port?
Do you need to authenticate?

use Bio::DB::GenBank;

my $db_obj = new Bio::DB::GenBank;
$db_obj->proxy(['http','ftp'], 'http://webgate.agresearch.co.nz:8080' );
$db_obj->authentication($user,$pass);

my $seq_obj=$db_obj->get_Seq_by_gi("42537818");

my $seqio_obj=Bio::SeqIO->new(-file => ">temp.txt", -format=> "fasta" );
$seqio_obj->write_seq($seq_obj);
	


Russell



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of ocar campos
> Sent: Wednesday, 30 July 2008 6:08 a.m.
> To: melody; bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] get_Seq_by_id: CONTIG found
> 
> 
> I got a very similar message when trying to access with a Version
Number, but
> saying that the sequence is not in the db, and when I check via web,
the sequence
> is there, and then the script works.
> 
> regards
> 
> O'car
> 
> ----------------------------------------
> > From: xyuany at mail2.sysu.edu.cn
> > To: bioperl-l at portal.open-bio.org
> > Date: Tue, 29 Jul 2008 23:47:31 -0700
> > Subject: [Bioperl-l]  get_Seq_by_id: CONTIG found
> >
> > I'm trying to download a bunch of sequences from GenBank using the
gi ,when
> > I run the code,I got The message like this :
> >
> > -------------------- WARNING ---------------------
> > MSG: CONTIG found. GenBank get_Stream_by_acc about to run.
> > ---------------------------------------------------
> > Warning: unable to close filehandle FETCH properly.
> >
> > What can I do if I want this code work.
> > Thanks a lot,
> > Melody xiong
> >
> >
> > use Bio::DB::GenBank;
> > my $db_obj = new Bio::DB::GenBank;
> > $db_obj->proxy(['http','ftp'],'http://proxy2.sysu.edu.cn:3128/');
> >         my $seq_obj=$db_obj->get_Seq_by_gi("42537818");
> >         my $seqio_obj=Bio::SeqIO->new(-file => ">temp2.txt", -format
=>
> > "fasta" );
> >         $seqio_obj->write_seq($seq_obj);
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
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