[Bioperl-l] get_Seq_by_id: CONTIG found

Kevin Brown Kevin.M.Brown at asu.edu
Tue Jul 29 15:44:48 EDT 2008


Might be a proxy server issue as I notice the code snippet uses one.

> -----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: Tuesday, July 29, 2008 11:08 AM
> 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);
> >         
> >  
> > 
> >  
> > 
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