[Bioperl-l] bptutorial.pl question, and appropriate bioperl version question

Chris Fields cjfields at uiuc.edu
Sun Mar 26 20:57:08 EST 2006


Try updating to at least v.1.5.1.  If that doesn't help, try updating  
from CVS.  Not sure if this has been reported as a bug or not but  
there have been many changes since 1.4 was released, many  
specifically in Blast parsing.  I'm not sure Bio::Perl is still using  
BPlite for Blast parsing but wouldn't be surprised if it has changed  
to SearchIO::blast.

Chris



On Mar 26, 2006, at 1:47 PM, Philip M Terry wrote:

>
> Hello,
>
> Would anyone be able to help/comment on the following:
>
> version of bioperl: Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
> (installed from CPAN)
> platform: Power Mac G5 OS X 10.4.5
> What trying to do: Practice/learn to run bptutorial.pl from
> ~/.cpan/build/bioperl-1.4, trying run_remoteblast
> Code that gives the error:
> philip-terrys-power-mac-g5:~/.cpan/build/bioperl-1.4 mterry$ perl -w
> bptutorial.pl 22
>
> Beginning run_remoteblast example...
> submitted Blast job
> retrieving results...      #line 3322 of bptutorial.pl
>
> -------------------- WARNING ---------------------
> MSG: Possible error (1) while parsing BLAST report!
> ---------------------------------------------------
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm
> line 337, <GEN3> line 30.
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm
> line 338, <GEN3> line 30.
> Use of uninitialized value in substitution (s///) at Bio/Tools/ 
> BPlite.pm
> line 339, <GEN3> line 30.
> Use of uninitialized value in pattern match (m//) at Bio/Tools/ 
> BPlite.pm
> line 341, <GEN3> line 30.
> philip-terrys-power-mac-g5:~/.cpan/build/bioperl-1.4 mterry$
>
> The variable $def never gets initialized at line 326 of BPlite.pm  
> module.
>
> I note that Bio::Tools::BPlite module will not to be supported in  
> future
> versions of bioperl.
>
> So should I go from bioperl ver 1.4 to ver 1.5.1 before proceeding to
> practice with bptutorial.pl?
>
> If so, do I need to delete/uninstall ver 1.4 first before  
> installing ver
> 1.5.1?  If so, how should it be done?
>
> Thanks,
> Philip M. Terry, Ph.D.
> University of Nebraska-Lincoln
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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