[Bioperl-l] get_Seq_by_acc() in Bio::DB::GeneBank failed

[jun hu]

Hi, QunFeng,
It solves the problem.
What cause this problem? Is it because NCBI changed its cgi location again?
Thanks a lot for the advice!
Best regards,
Jun Hu


>From: Qunfeng Dong <qfdong at iastate.edu>
>To: "jun hu" <junhu54 at hotmail.com>, bioperl-l at portal.open-bio.org
>Subject: Re: [Bioperl-l] get_Seq_by_acc()  in Bio::DB::GeneBank failed
>Date: Fri, 13 Jun 2003 14:29:03 -0500 (CDT)
>
>Heikki Lehvaslaiho helped me with the similar problem. You can try this:
>
>1. go to http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-
>live/Bio/DB/?cvsroot=bioperl
>
>2. download Bio::DB::{GenBank.pm&NCBIHelper.pm&WebDBSeqI.pm} and put them 
>into
>place like /usr/lib/perl5/site_perl/5.6.1/Bio/DB, where the originals are.
>
>Good luck.
>
>Qunfeng
>
>
> > Hi, Eveyone,
> > I just downloaded and installed bioperl on my linux 9 machine, after 
>that, I
> > tried test 1 to 22 of the bptutorial.pl. All test run fine except the 
>test
> > 11, the remote db access. I also tried the getGeneBank.pl script , the 
>same
> > error happened.
> > Error message
> >
> > ------------- EXCEPTION  -------------
> > MSG: acc does not exist
> > STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:176
> >
> > The debug is also tried, seems I never get anything from the buffer or
> > readline ...
> > I am wondering where or not the firewall is an issue? But I can use NCBI 
>web
> > site to find the gene that I am fetching by bioperl ...
> > Does anyone have any idea about this problem?
> >
> > Jun Hu
> > UMDNJ
> >
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> >
>
>
>Qunfeng Dong, Ph.D
>ZmDB Manager
>2104 Molecular Biology Building
>Iowa State University
>Ames, IA 50010
>
>
>
>
>
>
>
>

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