[Bioperl-l] Error when Using BLAT????

[Minh Bui]

Hi everyone,
I am writing an application that allows me to search through a database
(yeast.nt*) *with a few queries (yeastquery.fasta). Here is the code:

*use warnings;*
*use Bio::Tools::Run::Alignment::Blat;*
*use Bio::SeqIO;*
*use Bio::DB::Fasta;*
*  *
*my $seqio_object  = Bio::SeqIO -> new (-file =>
'C:/Users/MINH/Desktop/yeastquery.fasta',  -format => 'fasta'); *
*        *
*my $database = 'C:/Users/MINH/Desktop/yeast.nt';*
*my $db = Bio::DB::Fasta->new($database); *
*        *
*my $factory = Bio::Tools::Run::Alignment::Blat->new(); *
*
*
*while (my $blat_object = $seqio_object -> next_seq) {** *
*                my $results = $factory -> run($blat_object,$db); *
*}*


BUT i got this error and don't know how to fix it. I am sorry, i am new to
Perl and Bioperl. I am using window 7, Strawberry.


*Replacement list is longer than search list at
C:/strawberry/perl/site/lib/Bio/Range.pm line 251.*
*Use of uninitialized value in concatenation (.) or string at
C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm line 251, <GEN0>
line 1.*
*'-out' is not recognized as an internal or external command,*
*operable program or batch file.*
*
*
*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: Blat call ( -out=psl  C:\Users\MINH\AppData\Local\Temp\BUiXTGzYC2
C:\Users\MINH\AppData\Local\Temp\yQK5pzgJ_z) crashed: 256 *
*
*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw
C:/strawberry/perl/site/lib/Bio/Root/Root.pm:368*
*STACK: Bio::Tools::Run::Alignment::Blat::_run
C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:261*
*STACK: Bio::Tools::Run::Alignment::Blat::run
C:/strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Blat.pm:178*
*STACK: D:/eclipswp/bioperl/readfasta.pl:15*
*-----------------------------------------------------------*


Thank you for your help.