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

[Chris Fields]

On Jun 29, 2010, at 8:58 AM, Minh Bui wrote:

> 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.*

The above are warnings from perl 5.12 that can be ignored (they have been fixed in bioperl-live on github).

> *'-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.

That may be a bug; I can check on it (I'm planning on setting up a BLAT pipeline here in the next few days).

chris