[Bioperl-l] Running BLAT with BioPerl

Victor victor.ruotti at gmail.com
Thu Feb 9 23:22:11 UTC 2006

Does anyone know if the Bio/Tools/Run/Alignment/Blat.pm module is up to date
in the lastest bioperl release?

use Bio::Tools::Run::Alignment::Blat;
my $factory = Bio::Tools::Run::Alignment::Blat->new();
my $seq =

my @feats = $factory->run( $seq);

Here is what I get when tring to use it:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Blat call (/usr/local/bin/blat/blat -out=blast  TGAAATAAAACTCAGTA
/tmp/fB09bp5F76) crashed: -1

Notice that it is using "blat' twice in the path. The way that I fixed this
is by going to the blat.pm module and changing the following lines:
#my $str= Bio::Root::IO->catfile($self->executable,$self->program_name);
my $str= Bio::Root::IO->catfile($self->program_name);

Any ideas, maybe I'm missing the $ENV variable somewhere?
I'd like to avoid making this change. Also does anyone have a known synopsis
of this blat module (where to set the parameters, and whether it allows you
to have a config file).
I'll be happy to add a better synopsis to the module if needed.

Thanks in advance,

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