Raw content of Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPep
<![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::Compara::RunnableDB::BlastComparaPep
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $blast = Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPep->new
(
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$blast->fetch_input(); #reads from DB
$blast->run();
$blast->output();
$blast->write_output(); #writes to DB
=cut
=head1 DESCRIPTION
This object wraps Bio::EnsEMBL::Analysis::Runnable::Blast to add
functionality to read and write to databases.
The appropriate Bio::EnsEMBL::Analysis object must be passed for
extraction of appropriate parameters. A Bio::EnsEMBL::Analysis::DBSQL::Obj is
required for databse access.
=cut
=head1 CONTACT
Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPep;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Analysis::Runnable;
use Bio::EnsEMBL::Analysis::Runnable::Blast;
use Bio::EnsEMBL::Analysis::Tools::BPliteWrapper;
use Bio::EnsEMBL::Analysis::Tools::FilterBPlite;
use Bio::EnsEMBL::Hive::Process;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Hive::Process);
#
# our @ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Blast);
my $g_BlastComparaPep_workdir;
=head2 fetch_input
Title : fetch_input
Usage : $self->fetch_input
Function: Fetches input data for repeatmasker from the database
Returns : none
Args : none
=cut
sub fetch_input {
my( $self) = @_;
throw("No input_id") unless defined($self->input_id);
## Get the query (corresponds to the member with a member_id = input_id
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
my $member_id = $self->input_id;
my $member = $self->{'comparaDBA'}->get_MemberAdaptor->fetch_by_dbID($member_id);
throw("No member in compara for member_id = $member_id") unless defined($member);
if (10 > $member->bioseq->length) {
$self->input_job->update_status('DONE');
throw("BLAST : Peptide is too short for BLAST");
}
my $query = $member->bioseq();
throw("Unable to make bioseq for member_id = $member_id") unless defined($query);
## Get the db_file (defined in the analysis)
my $dbfile = $self->analysis->db_file;
## Define the filter from the parameters
my ($thr, $thr_type, $options);
#my $p = eval($self->analysis->parameters);
my $p = eval($self->analysis->data);
if (defined $p->{'-threshold'} && defined $p->{'-threshold_type'}) {
$thr = $p->{-threshold};
$thr_type = $p->{-threshold_type};
} else {
$thr_type = 'PVALUE';
$thr = 1e-10;
}
if (defined $p->{'options'}) {
$options = $p->{'options'};
} else {
$options = '';
}
## Create a parser object. This Bio::EnsEMBL::Analysis::Tools::FilterBPlite
## object wraps the Bio::EnsEMBL::Analysis::Tools::BPliteWrapper which in
## turn wraps the Bio::EnsEMBL::Analysis::Tools::BPlite (a port of Ian
## Korf's BPlite from bioperl 0.7 into ensembl). This parser also filter
## the results according to threshold_type and threshold.
my $regex = '^(\S+)\s*';
if ($p->{'regex'}) {
$regex = $p->{'regex'};
}
my $parser = Bio::EnsEMBL::Analysis::Tools::FilterBPlite->new(
-regex => $regex,
-query_type => "pep",
-input_type => "pep",
-threshold_type => $thr_type,
-threshold => $thr,
);
## Create the runnable with the previous parser. The filter is not required
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Blast->new(
-query => $query,
-database => $dbfile,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
-options => $options,
-parser => $parser,
-filter => undef,
);
$self->runnable($runnable);
return 1;
}
=head2 runnable
Arg[1] : (optional) Bio::EnsEMBL::Analysis::Runnable $runnable
Example : $self->runnable($runnable);
Function : Getter/setter for the runnable
Returns : Bio::EnsEMBL::Analysis::Runnable $runnable
Exceptions : none
=cut
sub runnable {
my $self = shift(@_);
if (@_) {
$self->{_runnable} = shift;
}
return $self->{_runnable};
}
=head2 run
Arg[1] : -none-
Example : $self->run;
Function : Runs the runnable set in fetch_input
Returns : 1 on succesfull completion
Exceptions : dies if runnable throws an unexpected error
=cut
sub run {
my $self = shift;
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);
## call runnable run method in eval block
eval { $self->runnable->run(); };
## Catch errors if any
if ($@) {
printf(STDERR ref($self->runnable)." threw exception:\n$@$_");
if($@ =~ /"VOID"/) {
printf(STDERR "this is OK: member_id=%d doesn't have sufficient structure for a search\n", $self->input_id);
} else {
die("$@$_");
}
}
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
return 1;
}
sub write_output {
my( $self) = @_;
#since the Blast runnable takes in analysis parameters rather than an
#analysis object, it creates new Analysis objects internally
#(a new one for EACH FeaturePair generated)
#which are a shadow of the real analysis object ($self->analysis)
#The returned FeaturePair objects thus need to be reset to the real analysis object
foreach my $feature (@{$self->output}) {
if($feature->isa('Bio::EnsEMBL::FeaturePair')) {
$feature->analysis($self->analysis);
}
}
$self->{'comparaDBA'}->get_PeptideAlignFeatureAdaptor->store(@{$self->output});
}
sub output {
my ($self, @args) = @_;
throw ("Cannot call output without a runnable") if (!defined($self->runnable));
return $self->runnable->output(@args);
}
sub global_cleanup {
my $self = shift;
if($g_BlastComparaPep_workdir) {
unlink(<$g_BlastComparaPep_workdir/*>);
rmdir($g_BlastComparaPep_workdir);
}
return 1;
}
##########################################
#
# internal methods
#
##########################################
# using the genome_db and longest peptides subset, create a fasta
# file which can be used as a blast database
sub dumpPeptidesToFasta
{
my $self = shift;
my $startTime = time();
#my $params = eval($self->analysis->parameters);
my $params = eval($self->analysis->data);
my $genomeDB = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($params->{'genome_db_id'});
# create logical path name for fastafile
my $species = $genomeDB->name();
$species =~ s/\s+/_/g; # replace whitespace with '_' characters
#create temp directory to hold fasta databases
$g_BlastComparaPep_workdir = "/tmp/worker.$$/";
mkdir($g_BlastComparaPep_workdir, 0777);
my $fastafile = $g_BlastComparaPep_workdir.
$species . "_" .
$genomeDB->assembly() . ".fasta";
$fastafile =~ s/\/\//\//g; # converts any // in path to /
return $fastafile if(-e $fastafile);
print("fastafile = '$fastafile'\n");
# write fasta file to local /tmp/disk
my $subset = $self->{'comparaDBA'}->get_SubsetAdaptor()->fetch_by_dbID($params->{'subset_id'});
$self->{'comparaDBA'}->get_SubsetAdaptor->dumpFastaForSubset($subset, $fastafile);
# configure the fasta file for use as a blast database file
my $blastdb = new Bio::EnsEMBL::Analysis::Runnable::BlastDB (
-dbfile => $fastafile,
-type => 'PROTEIN');
$blastdb->run;
print("registered ". $blastdb->dbname . " for ".$blastdb->dbfile . "\n");
printf("took %d secs to dump database to local disk\n", (time() - $startTime));
return $fastafile;
}
1;
]]>