[Bioperl-l] Blat running/parsing problem

[Holger Klein]

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Hello all,

I have a problem using blat from within bioperl-run.

Using

<code>
my $inseq = Bio::SeqIO->new(
	'-file'   => "<$queryfile",
	'-format' => "fasta" );

my $seq = $inseq->next_seq;
my $seqname = $seq->id();
# $subject is a string containing the location of another fasta file
my $blat_fac = Bio::Tools::Run::Alignment::Blat->new(
	"program_dir" => $BLAT_dir,
	"DB" => $subject) ;
my @feats = $blat_fac->run($seq);

for my $f (@feats) {
	while (my $r = $f->next_result()) {
       		print $r."\n";
	}
</code>

I get the following error message:

- -->%--
Argument "2.2.4" isn't numeric in addition (+) at 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, 
<GEN4> line 1.
Argument "BLASTN" isn't numeric in addition (+) at 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, 
<GEN4> line 1.
Argument "[blat]" isn't numeric in addition (+) at 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, 
<GEN4> line 1.
Use of uninitialized value in division (/) at 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, 
<GEN4> line 1.
Illegal division by zero at 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/SearchIO/psl.pm line 191, 
<GEN4> line 1.
- --%<--

Looking at the output of the blat run, it seems as if it was called with 
   the option -out=blast by bioperl, while $f, the element which is 
given back from $blat_fac->run($seq) above is of type 
Bio::SearchIO::psl=HASH(0x858ad8c). So it seems to me, that 
Bio::Tools::Run::Alignment::Blat tries to parse blast-like output with a 
psl-parser.
I tried to give an output type parameter to my blat-factory with:
<code>
my $blat_fac = Bio::Tools::Run::Alignment::Blat->new(
	"program_dir" => $BLAT_dir,
	"DB" => $subject,
	"out" => "psl");
</code>

which resulted in:
- -->%--
- ------------- EXCEPTION  -------------
MSG: Unallowed parameter: OUT !
STACK Bio::Tools::Run::Alignment::Blat::AUTOLOAD 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Alignment/Blat.pm:110
STACK Bio::Tools::Run::Alignment::Blat::new 
/usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Alignment/Blat.pm:137
- --%<--

Can anybody tell me what I'm doing wrong here or point me to a piece of 
code, where I can see how running blat and parsing it's output is really 
done?

BTW: all of this happens in bioperl-run-1.4 and bioperl-1.4.

Regards,
Holger


- -- 
Holger Klein
computational molecular biology - MPI for molecular genetics
http://www.molgen.mpg.de/~klein_h | room #334
holger.klein at molgen.mpg.de        | fon +49 (0)30 8413-1170 / fax -1152
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