Raw content of Bio::EnsEMBL::Analysis::RunnableDB::BlastGenscanPep
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::BlastGenscanPep
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Blast
=head1 SYNOPSIS
my $blast = Bio::EnsEMBL::Analysis::RunnableDB::BlastGenscanPep->
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
This module inherits from the Blast runnable and instantiates
BlastTranscriptPep passing in prediction transcript
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::BlastGenscanPep;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::Runnable::BlastTranscriptPep;
use Bio::EnsEMBL::Analysis::RunnableDB::Blast;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Analysis::Config::Blast;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Blast);
=head2 fetch_input
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::BlastGenscanPep
Function : fetch sequence and prediction transcripts of database,
read config files instantiate the filter, parser and finally the blast
runnables
Returntype: none
Exceptions: none
Example :
=cut
sub fetch_input{
my ($self) = @_;
my $slice = $self->fetch_sequence($self->input_id, $self->db);
$self->query($slice);
my %blast = %{$self->BLAST_PARAMS};
my $logic_name = $BLAST_AB_INITIO_LOGICNAME;
$logic_name = 'Genscan' if(!$logic_name);
my $pta = $self->db->get_PredictionTranscriptAdaptor;
my $pts = $pta->fetch_all_by_Slice($self->query, $logic_name);
my $parser = $self->make_parser;
my $filter;
if($self->BLAST_FILTER){
$filter = $self->make_filter;
}
foreach my $t(@$pts){
my $runnable = Bio::EnsEMBL::Analysis::Runnable::BlastTranscriptPep->
new(
-transcript => $t,
-query => $self->query,
-program => $self->analysis->program_file,
-parser => $parser,
-filter => $filter,
-database => $self->analysis->db_file,
-analysis => $self->analysis,
%blast,
);
$self->runnable($runnable);
}
}
]]>