Raw content of Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Blast
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam
=head1 SYNOPSIS
my $blast = Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam->
new(
-analysis => $analysis,
-db => $db,
-input_id => 'contig::AL1347153.1.3517:1:3571:1'
);
$blast->fetch_input;
$blast->run;
my @output =@{$blast->output};
=head1 DESCRIPTION
Modified blast runnable for specific use with RFAMSEQ.
Use for running BLASTN of genomic vs RFAMSEQ prior to
ncRNA analysis using Infernal.
Slice size seems best around 200k
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::BlastRfam;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB::Blast;
use Bio::EnsEMBL::Analysis::Runnable::BlastRfam;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Blast;
use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use Bio::EnsEMBL::Analysis::Config::Databases qw(DATABASES DNA_DBNAME);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Blast Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild);
=head2 fetch_input
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::Blast
Function : fetch sequence out of database, instantiate the filter,
parser and finally the blast runnable
Returntype: 1
Exceptions: none
Example :
=cut
sub fetch_input{
my ($self) = @_;
# attach dna-db to db
my $dna_db = $self->get_dbadaptor($DNA_DBNAME);
$self->db->dnadb($dna_db);
my $slice = $self->fetch_sequence($self->input_id, $self->db,['Dust']);
$self->query($slice);
my %blast = %{$self->BLAST_PARAMS};
my $parser = $self->make_parser;
my $filter;
if($self->BLAST_FILTER){
$filter = $self->make_filter;
}
my $seq = $self->query;
my $runnable = Bio::EnsEMBL::Analysis::Runnable::BlastRfam->new
(
-query => $seq,
-program => $self->analysis->program_file,
-parser => $parser,
-filter => $filter,
-database => $self->analysis->db_file,
-analysis => $self->analysis,
-params => \%blast,
);
$self->runnable($runnable);
return 1;
}
]]>