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

[Qunfeng Dong]

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