Bio::EnsEMBL::Analysis::RunnableDB
miRNA
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Summary
Bio::EnsEMBL::Analysis::RunnableDB::miRNA
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $runnableDB = Bio::EnsEMBL::Analysis::RunnableDB::miRNA->new(
-db => $db_adaptor,
-input_id => 'analysis logic name',
-analysis => $analysis,
);
$runnabledb->fetch_input();
$runnabledb->run();
$runnabledb->write_output();
Description
RunnableDB to provide database access for miRNA detection.
Runs as an accumulator job on miRNA blast hits found by Bio::EnsEMBL::RunnableDB::BlastmiRNA
Takes an analysis logic name as an input id and uses it to fetch all dna align features associated with
that analysis.
It then groups the dna align features by miRNA families and ignores families with > 50
members as there is a high probability that these are hitting repetitive sequences.
Creates and runs the miRNA runnable.
Methods
Methods description
Title : family
Usage : my %families = %{$self->family(\@dafs)};
Function : order dafs by family, removes families with blast hits to repeats
Returns : Hash reference
Exceptions : None
Args : Array ref of Bio::EnsEMBL::DnaDnaAlignFeatures |
Title : fetch_input
Usage : $miRNA->fetch_input();
Function : opens and stores connections to databases in Bio::EnsEMBL::Analysis::Config::Databases
: fetches all dna align features by analysis logic name specified in the
: input id
Returns : Hash reference
Exceptions : throws if the analysis object is not found or no dna align features are retrieved
Args : None |
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
Description: get/set gene db adaptor
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : general |
Args : none
Description: Writes the single exon miRNA genes into the final genebuild database,
: also stores attributes associated with the transcript
Exceptions : Throws if gene or transcript attribute fail to write to the database
Returntype : scalar |
Methods code
sub family
{ my ($self,$dafs_ref) = @_;
my %families;
foreach my $daf (@$dafs_ref){
push @{$families{$daf->hseqname}},$daf;
}
my %filtered_fam;
foreach my $key (keys %families){
if (scalar @{$families{$key}} <= 50){
$filtered_fam{$key} = $families{$key};
} else {
my @array = sort {$a->p_value <=> $b->p_value} @{$families{$key}};
my @filtered_array = splice(@array,0,50);
$filtered_fam{$key} =\@ filtered_array;
}
}
return\% filtered_fam;} | sub fetch_input
{ my ($self) = @_;
my $dna_db = $self->get_dbadaptor($DNA_DBNAME) ;
if ( $$DATABASES{'GENEBUILD_DB'}{'-dbname'} eq $self->db->dbc->dbname &&
$$DATABASES{'GENEBUILD_DB'}{'-port'} == $self->db->dbc->port &&
$$DATABASES{'GENEBUILD_DB'}{'-host'} eq $self->db->dbc->host){
$self->gene_db($self->db);
} else {
my $genes_db = $self->get_dbadaptor("GENEBUILD_DB");
$self->gene_db($genes_db);
}
$self->db->dnadb($dna_db);
my $aa = $self->db->get_AnalysisAdaptor;
my $analysis = $aa->fetch_by_logic_name($self->input_id);
$self->throw("Analysis BlastmiRNA not found $@\n") unless $analysis;
my $dafa = $self->db->get_DnaAlignFeatureAdaptor;
my @flags;
my @dafs;
my $fa = Bio::EnsEMBL::Pipeline::DBSQL::FlagAdaptor->new($self->db);
print "Fetching features\n";
eval{
@flags = @{$fa->fetch_by_analysis($self->analysis)};
};
foreach my $flag (@flags){
if ($flag->goalAnalysis->logic_name eq $self->analysis->logic_name){
my $daf = $dafa->fetch_by_dbID($flag->ensembl_id);
push @dafs, $daf;
}
}
$self->throw("No dna align features found ") unless (scalar(@dafs) >=1);
print scalar(@dafs)." dafs found\n";
my %families = %{$self->family(\@dafs)};
@dafs = ();
my $runnable = Bio::EnsEMBL::Analysis::Runnable::miRNA->new
(
-queries =>\% families,
-analysis => $self->analysis,
);
$self->runnable($runnable); } | sub gene_db
{ my ($self, $gene_db) = @_;
if ($gene_db){
unless ($gene_db->isa("Bio::EnsEMBL::DBSQL::DBAdaptor")){
$self->throw("gene db is not a Bio::EnsEMBL::DBSQL::DBAdaptor, it is a $gene_db");
}
$self->{'_gene_db'} = $gene_db;
}
return $self->{'_gene_db'};
}
1;} | sub write_output
{ my ($self) = @_;
my $adaptor = $self->gene_db->get_GeneAdaptor;
my $aa = $self->gene_db->get_AttributeAdaptor;
my @attributes;
my $xref;
foreach my $gene_hash (@{$self->output}){
my $gene = $gene_hash->{'gene'};
@attributes = @{$gene_hash->{'attrib'}};
$gene->analysis($self->analysis);
$gene->status('PREDICTED');
foreach my $trans (@{$gene->get_all_Transcripts}){
$trans->analysis($self->analysis);
$trans->status('PREDICTED');
}
$gene->slice($self->query) if(!$gene->slice);
$self->feature_factory->validate($gene);
eval{
$adaptor->store($gene);
print STDERR "Attemting to store in ".$adaptor->db->dbname."\n";
};
if($@){
$self->throw("miRNA:store failed, failed to write ".$gene." to ".
"the database $@");
}
foreach my $trans (@{$gene->get_all_Transcripts}){
eval{
$aa->store_on_Transcript($trans->dbID,\@attributes);
$self->gene_db->get_TranscriptAdaptor->update($trans);
$self->gene_db->get_GeneAdaptor->update($gene);
};
if($@){
$self->throw("miRNA:store failed, failed to write ".@attributes." on transcript ".
$trans." in the database $@");
}
}
}
return 1;
}
} | General documentation