[Bioperl-l] error with blast parsing by searchIO

Chris Fields cjfields at uiuc.edu
Sun Apr 15 13:40:24 EDT 2007


You have to update to bioperl 1.5.2 or CVS.  BLAST parsing is broken  
for recent BLAST versions (> v.2.2, I believe).

chris

On Apr 15, 2007, at 11:13 AM, sergei ryazansky wrote:

> Hello all,
>
> script (parsing blastn report) that previously had worked today  
> "tell" me
> that:
>
> ------------- EXCEPTION  -------------
> MSG: Could not open BLASTN 2.2.13 [Nov-27-2005]
> : No such file or directory
> STACK Bio::Root::IO::_initialize_io c:/Perl/site/lib/Bio/Root/IO.pm: 
> 273
> STACK Bio::Root::IO::new c:/Perl/site/lib/Bio/Root/IO.pm:213
> STACK Bio::SearchIO::new c:/Perl/site/lib/Bio/SearchIO.pm:135
> STACK Bio::SearchIO::new c:/Perl/site/lib/Bio/SearchIO.pm:167
> STACK toplevel parse-te-lib2.pl:3
>
> --------------------------------------
>
> What does it mean??
>
> ps. bioperl-1.4 with ActivePerl 5.8.7&5.8.8
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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





More information about the Bioperl-l mailing list