[Bioperl-l] Using BLAT in BioPerl

oso oso.oro at gmail.com
Sun Dec 14 20:33:45 EST 2008


I am using the BioPerl module  Bio::Tools::Run::Alignment::Blat to run
standalone BLATs.  The search I am doing works fine if I do it from a normal
command line interface.  The same sequences and genome are not working in
the BioPerl interface.  I think my problem might be how I defined the
database, as it it isn't showing up in the resulting BLAT call.  Does anyone
see my problem?

Find scripting below.

my $seqio_object  = Bio::SeqIO -> new (-file => 'reads1.fa',
												 -format => 'fasta'); 
my $database = 'chr2.fa';
my $db = Bio::DB::Fasta->new($database);
my $factory = Bio::Tools::Run::Alignment::Blat->new();

#sets up a do-while loop as long as I still have sequences to blast
while (my $blat_object = $seqio_object -> next_seq) {		
		my $results = $factory -> run($blat_object,$db);
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