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

[Feng Sun]

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'  );

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