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

[Feng Sun]

Thanks! Jason. I am clear now. I will use lavToPsl. 

-- 
Feng Sun

On Wed, 10 Dec 2003, Jason Stajich wrote:

> 
> On Wed, 10 Dec 2003, 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.
> 
> I'm confused - you are using the psl format SearchIO module and you're
> wondering why you need to pass in psl format data?
> 
> You need to run lavToPsl to turn the blastz output into psl, as we don't
> make an effor to parse BLASTZ's lav natively.
> (http://www.cse.ucsc.edu/~kent/src/unzipped/hg/mouseStuff/lavToPsl/)
> 
> The -program_name => 'BLASTZ' is a convience for the type of features that
> are created (source_tag is getting filled with $program_name).
> 
> [From mail message where I introduced the SearchIO::psl module
> http://portal.open-bio.org/pipermail/bioped-l/2003-August/000016.html]
> 
> [Bio::SearchIO]
> Added some more SearchIO parsers.  Borrowing from Bala's Tools::Blat
> impelementation I made a SearchIO::psl parser which can parse PSL output.
> It needs to be tweaked a little more to skip the header lines if they are
> produced but works for me for output from Jim's lav2Psl code.
> 
> 
> >
> > 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!
> >
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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