Raw content of Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation
<![CDATA[
=head1 NAME
ProteinAnnotation.pm - DESCRIPTION of Object
=head1 SYNOPSIS
this is the base class for the ProteinAnnotation runnabledbs
=head1 DESCRIPTION
=head1 CONTACT
ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
use Bio::EnsEMBL::Analysis::Config::ProteinAnnotation;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw (Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild);
################################
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
throw("Analysis object required") unless ($self->analysis);
$self->read_and_check_config;
return $self;
}
################################
sub fetch_input {
my ($self) = @_;
my $input_id;
my $db;
if ($self->GENEDB) {
$db = $self->get_dbadaptor($self->GENEDB);
} else {
$db = $self->db;
}
my $error = "For logic " . $self->analysis->logic_name . ", Input id must be:\n";
$error .= "(a) a valid translation dbID; or\n";
$error .= "(b) the fully qualified directory/name of a fasta peptide file; or\n";
$error .= "(c) the name only of a peptide fasta file (with BASE_DIR defined)\n";
$error .= $self->input_id . " is none of these\n";
if ($self->input_id =~ /^(\d+)$/) {
my $prot;
eval {
$prot = $db->get_TranslationAdaptor->fetch_by_dbID($self->input_id);
};
if($@ or not defined $prot) {
throw($error);
}
$input_id = Bio::PrimarySeq->new(-seq => $prot->seq,
-id => $self->input_id,
-accession => $self->input_id,
-moltype => 'protein');
} elsif ($self->input_id =~ /^\// and -e $self->input_id) {
# assume fully-qualified file name
$input_id = $self->input_id;
} elsif (defined $self->BASE_DIR and
$self->BASE_DIR and
-e $self->BASE_DIR . "/" . $self->input_id) {
$input_id = $self->BASE_DIR . "/" . $self->input_id;
} else {
throw($error);
}
$self->query($input_id);
}
##################################
sub write_output {
my($self) = @_;
my @features = @{$self->output()};
my $db;
if ($self->GENEDB) {
$db = $self->get_dbadaptor($self->GENEDB);
} else {
$db =$self->db;
}
my $adap = $db->get_ProteinFeatureAdaptor;
foreach my $feat(@features) {
$adap->store($feat, $feat->seqname);
}
return 1;
}
##################################
sub run {
my ($self,$dir) = @_;
throw("Runnable module not set") unless ($self->runnable());
my $db;
if ($self->GENEDB) {
$db = $self->get_dbadaptor($self->GENEDB);
} else {
$db =$self->db;
}
$db->dbc->disconnect_when_inactive(1);
my ($run) = @{$self->runnable};
$run->run($dir);
$db->dbc->disconnect_when_inactive(0);
$self->output($run->output);
}
###################################
sub query{
my ($self, $query) = @_;
if(defined $query){
if (ref($query)) {
if (not $query->isa('Bio::PrimarySeqI')) {
throw("Must pass RunnableDB:query a Bio::PrimarySeqI "
. "not a ".$query);
}
} elsif (not -e $query) {
throw("Must pass RunnableDB::query a filename that exists " . ref($query));
}
$self->{_query} = $query;
}
return $self->{_query};
}
#####################################
sub output {
my ($self, $output) = @_;
if(!$self->{'output'}){
$self->{'output'} = [];
}
if($output){
if(ref($output) ne 'ARRAY'){
throw('Must pass RunnableDB:output an array ref not a '.$output);
}
$self->{'output'} = $output;
}
return $self->{'output'};
}
####################################
#############################################################
# Declare and set up config variables
#############################################################
sub read_and_check_config {
my $self = shift;
$self->SUPER::read_and_check_config($PROTEINANNOTATION_CONFIG_BY_LOGIC);
##########
# CHECKS
##########
my $logic = $self->analysis->logic_name;
# check that compulsory options have values
if (defined $self->BASE_DIR and
$self->BASE_DIR and
not -d $self->BASE_DIR) {
throw("BASE_DIR " . $self->BASE_DIR . " could not be found")
}
}
sub BASE_DIR {
my ($self, $val) = @_;
if (defined $val) {
$self->{_base_dir} = $val;
}
if (not exists $self->{_base_dir}) {
return undef;
} else {
return $self->{_base_dir};
}
}
sub GENEDB {
my ($self, $val) = @_;
if (defined $val) {
$self->{_gene_db} = $val;
}
if (not exists $self->{_gene_db}) {
return undef;
} else {
return $self->{_gene_db};
}
}
1;
]]>