[Bioperl-l] bioperl installation on fedora core 5

Chris Fields cjfields at uiuc.edu
Fri Sep 8 17:26:24 EDT 2006


You will likely need to update to CVS for proper BLAST parsing, especially
if it is using a remote blast (I can't remember bp #5 off the top of my
head).  NCBI had changed BLAST output formatting which broke BLAST parsing
in bioperl 1.5.1.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of GeOrgE RosEnbERg
> Sent: Friday, September 08, 2006 4:05 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] bioperl installation on fedora core 5
> 
> Dear Bioperl,
> 
> I have installed bioperl 1.5.1 on a fedora core 5 x64 machine and I am
> having problems parsing information out of blast reports.
> 
> I went back and started to run bptutorial.pl and I am getting the
> following
> error when running #5:
> 
> Beginning example of sequence manipulation without explicit Seq objects...
> 
> -------------------- WARNING ---------------------
> MSG: id (ROA1_HUMAN) does not exist
> ---------------------------------------------------
> Can't call method "display_id" on an undefined value at bptutorial.pl line
> 3945.
> 
> Could this error be related to my parsing problem or show that I have not
> installed bioperl correctly?
> 
> Thank you,
> 
> George
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