[Bioperl-l] Fwd: blast result not matching.

Fields, Christopher J cjfields at illinois.edu
Wed Sep 7 12:33:52 EDT 2011


I think there was an issue with Bio::Perl BLAST submissions fixed in the 1.6.901 release (1.6.9 != 1.6.901, the latter is newer).  From CPAN:

1.6.901 May 18, 2011

...

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]

chris

On Sep 7, 2011, at 11:13 AM, Jason Stajich wrote:

> I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
> Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.
> 
> 
> On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:
> 
>> bioperl 1.6.9 version is installed in my system..
>> its not the reason bcs blast is working fine when i am blasting with
>> follwing code..
>> 
>> #!usr/bin/perl -w
>> use Bio::Perl;
>> $seq = get_sequence('NCBI',"NM_181451");
>> $blast_result=blast_sequence($seq);
>> write_blast(">xyz.blast",$blast_result);
>> 
>> 
>> Manju
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




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