[Bioperl-l] get_Seq_by_id: CONTIG found

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jul 29 18:17:33 EDT 2008


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
> 
> _________________________________________________________________
> Invite your mail contacts to join your friends list with Windows Live
Spaces. It's
> easy!
>
http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.a
spx&m
> kt=en-us
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



More information about the Bioperl-l mailing list