[Bioperl-l] get_Seq_by_id: CONTIG found

ocar campos ocar1987 at hotmail.com
Tue Jul 29 14:07:58 EDT 2008


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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