[Bioperl-l] error with blast parsing by searchIO

sergei ryazansky dr.hogart at gmail.com
Mon Apr 16 03:03:46 EDT 2007


The problem was resolved by the direct path (-file=>'d\...\input.txt') to  
input file in the my script.
I think that Chris right and i should update my bioperl to 1.5 version.
By the way, bioperl-1.5 is not accessible via ppm. Where I can download it  
for winXP?

On Sun, 15 Apr 2007 22:24:56 +0400, Jason Stajich <jason at bioperl.org>  
wrote:

> It looks like something is broken in your script as to how you are
> passing it a filename - it is trying to open a file called "BLASTN
> 2.2.13 [Nov-27-2005]".
> did you already open the file and are you passing data from the first
> line of the file to SearchIO perhaps?
> Sending the relevant part of your script to the list will help us
> diagnose the problem better.
>
> -jason
> On Apr 15, 2007, at 9:13 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
>
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
>
>



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