Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Finished::Blast
<![CDATA[# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Finished::Blast
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBLoader->new($locator);
my $blast = Bio::EnsEMBL::Analysis::RunnableDB::Blast->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$blast->fetch_input();
$blast->run();
$blast->output();
$blast->write_output(); #writes to DB
=head1 DESCRIPTION
This object wraps Bio::EnsEMBL::Analysis::Runnable::Blast to add
functionality for reading and writing to databases.
The appropriate Bio::EnsEMBL::Analysis object must be passed for
extraction of appropriate parameters. A Bio::EnsEMBL::Pipeline::DBSQL::Obj is
required for databse access.
=head1 CONTACT
Modified by Sindhu K. Pillai B<email> sp1@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Finished::Blast;
use strict;
use Bio::EnsEMBL::Analysis::Runnable::Finished::Blast;
use Bio::EnsEMBL::Pipeline::SeqFetcher::Finished_Pfetch;
use Bio::EnsEMBL::Analysis::Config::Blast;
use Bio::EnsEMBL::Analysis::Config::General;
use base (
'Bio::EnsEMBL::Analysis::RunnableDB::Blast',
'Bio::EnsEMBL::Analysis::RunnableDB::Finished'
);
sub fetch_input {
my ($self) = @_;
my $slice =
$self->fetch_sequence( $self->input_id, $self->db,
$ANALYSIS_REPEAT_MASKING, $SOFT_MASKING );
$self->query($slice);
my %blast = %{ $self->BLAST_PARAMS };
my $parser = $self->make_parser;
my $filter;
if ( $self->BLAST_FILTER ) {
$filter = $self->make_filter;
}
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Finished::Blast->new(
-query => $self->query,
-program => $self->analysis->program,
-parser => $parser,
-filter => $filter,
-database => $self->analysis->db_file,
-analysis => $self->analysis,
%blast,
);
my $s = $self->runnable($runnable);
return 1;
}
sub _createfiles {
my ( $self, $dirname, $filenames ) = @_;
my $unique = {};
$unique = { map { $_, $unique->{$_}++ } @$filenames };
my @files = ();
$dirname ||= '/tmp';
$dirname =~ s!(\S+)/$!$1!;
foreach my $file (@$filenames) {
if ( $unique->{$file} ) {
#name not unique add random
$file .= ".$$." . int( rand(200) );
push( @files, "$dirname/$file" );
}
else {
#name was unique just add it
push( @files, "$dirname/$file.$$" );
}
}
return @files;
}
=head2 run
Title : write_output
Usage : $self->write_output();
Function: Writes Features , hit_descriptions to database by calling parent write_output method
Returns : none
Args : none
=cut
sub write_output {
my ($self) = @_;
$self->Bio::EnsEMBL::Analysis::RunnableDB::Finished::write_output();
return 1;
}
=head2 db_version_searched
Title : db_version_searched
[ distinguished from Runnable::*::get_db_version() ]
Useage : $self->db_version_searched('version string')
$obj->db_version_searched()
Function: Get/Set a blast database version that was searched
The actual look up is done in Runnable::Finished::Blast
This is just a holding place for the string in this
module
Returns : String or undef
Args : String
Caller : $self::run()
Job::run_module()
=cut
sub db_version_searched {
my ( $self, $arg ) = @_;
$self->{'_db_version_searched'} = $arg if $arg;
return $self->{'_db_version_searched'};
}
1;
]]>