[Bioperl-l] Can Bio::SearchIO::psl.pm parse BlastZ output?

[Wes Barris]

Feng Sun wrote:
> Hi Folks,
> 
> I am using Bioperl1.303 to parse BlastZ(blastz-2003-05-14.tar.gz) output.
> But it looks like the psl.pm treat blastz file as psl file.
> 
> Here is how I create the SearchIO object:
>  
> $searchin = new Bio::SearchIO( -file => $file,
>                                         -format => 'psl',
>                                         -program_name => 'BLASTZ'  );

Perhaps I am missing something but I thought that blastz outputs .lav
format not .psl format.  Blat, outputs .psl files.

> 
> Here is the error message:
> 
> Argument "" isn't numeric in addition (+) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/psl.pm line 191, <GEN2> line
> 1.
> Argument "#:lav" isn't numeric in addition (+) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/psl.pm line 191, <GEN2> line
> 1.
> Use of uninitialized value in addition (+) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/psl.pm line 191, <GEN2> line
> 1.
> Use of uninitialized value in division (/) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/psl.pm line 191, <GEN2> line
> 1.
> Illegal division by zero at
> /usr/lib/perl5/site_perl/5.6.1/Bio/SearchIO/psl.pm line 191, <GEN2> line
> 1.
> 
> Here is line 191 in psl.pm:
>        my $score   = sprintf "%.2f", ( 100 * ( $matches + $mismatches +
> $rep_matches ) / $q_length );
> 
> The "$matches", "$mismatches" and "$rep_matches" are all fields in psl
> files. Also, I can't find anything in psl.pm indicating that it use the
> "-program_name => 'BLASTZ'" information to treat BlastZ files differently.
> 
> Has anyone used this module to parse BlastZ output correctly? If yes,
> which version of Bioperl are you using? Thanks for your help!
> 
> -- 
> Feng Sun
> 
> Laboratory for Genomics and Bioinformatics
> The University of Georgia, Department of Plant Biology
> Plant Sciences Building, Rm. 2502,
> Athens, GA 30602-7271, USA
> Tel:(706)5830791
> 
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> 


-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au