Bio::EnsEMBL::Analysis::RunnableDB Finished
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Package variables
Privates (from "my" definitions)
%ana2extdbid = ( Uniprot_raw => { "." => 2250 }, Uniprot_SW => { "-" => 2202 , "^\\w+\\.\\d+" => 2200 }, Uniprot_TR => { "." => 2000 }, default => { "." => 700 }, refseq => { "M_" => 1800, "P_" => 1810, "R_" => 1820, "^(AC|N[CGTWSZ])_" => 1830 } )
Included modules
Bio::EnsEMBL::Pipeline::SeqFetcher::Finished_Dfetch
Bio::EnsEMBL::Utils::Exception qw ( verbose throw warning )
Inherit
Bio::EnsEMBL::Analysis::RunnableDB
Synopsis
No synopsis!
Description
No description!
Methods
get_adaptor
No description
Code
get_extdb_id
No description
Code
get_feature_key
No description
Code
output
No description
Code
remove_all_features
No description
Code
remove_stored_AlignFeatures
No description
Code
replace_output
No description
Code
write_descriptions
No description
Code
write_output
No description
Code
Methods description
None available.
Methods code
get_adaptordescriptionprevnextTop
sub get_adaptor {
	my ($self, $feat) = @_;

	if ( $feat->isa('Bio::EnsEMBL::DnaPepAlignFeature') ) {
		return $self->db->get_ProteinAlignFeatureAdaptor;
	}
	elsif ( $feat->isa('Bio::EnsEMBL::DnaDnaAlignFeature') ) {
		return $self->db->get_DnaAlignFeatureAdaptor;
	}
    elsif ( $feat->isa('Bio::EnsEMBL::SimpleFeature') ) {
        return $self->db->get_SimpleFeatureAdaptor;
    }
	else {
		throw('unexpected feature type: '. ref($feat));
	}
}

1;
}
get_extdb_iddescriptionprevnextTop
sub get_extdb_id {
	my ($self, $logic_name, $hit_name) = @_;
	my $hash;
	# get the right analysis hash
foreach (keys %ana2extdbid) { if( $logic_name =~ /$_/ ) { $hash = $ana2extdbid{$_}; } } $hash = $ana2extdbid{default} unless $hash; # check the hit_name
foreach (keys %$hash) { if( $hit_name =~ /$_/ ){ return $hash->{$_}; } } throw("Cannot get external_db id for hit $hit_name and analysis $logic_name\n");
}
get_feature_keydescriptionprevnextTop
sub get_feature_key {
	my ( $self, $feat, $uni ) = @_;
	throw(
"Must pass Bio::EnsEMBL::Analysis::RunnableDB::Finished::get_feature_key a Bio::EnsEMBL::BaseAlignFeature"
		  . "not a "
		  . $feat )
	  unless ( $feat->isa('Bio::EnsEMBL::BaseAlignFeature') );
	my $name = $feat->display_id;
	$name =~ s/\.\d// if($uni);
	return join( ':',
		$name, $feat->seq_region_name, $feat->cigar_string,
		$feat->start, $feat->end, $feat->hstart, $feat->hend );
}
outputdescriptionprevnextTop
sub output {
  my ($self, @output) = @_;
  if(!$self->{'output'}){
    $self->{'output'} = [];
  }
  if(scalar(@output)){
    push(@{$self->{'output'}}, @output);
  }
  if(ref($self->{'output'}->[0]) ne 'ARRAY')
  {
  	return [ $self->{'output'} ] ;
  }
  return $self->{'output'};
}
remove_all_featuresdescriptionprevnextTop
sub remove_all_features {
	my ($self, $adaptor) = @_;
	my $db_features =
      $adaptor->fetch_all_by_Slice($self->query, $self->analysis->logic_name);
    foreach my $f (@$db_features) { $adaptor->remove($f);}
    print STDOUT "Finished: Removed ", scalar(@$db_features), " features through ".ref($adaptor)."\n ";
}
remove_stored_AlignFeaturesdescriptionprevnextTop
sub remove_stored_AlignFeatures {
    my ($self, $adaptor, $output, $all) = @_;
	## create a hashtable of the contig hits stored in the database
my $db_features = $adaptor->fetch_all_by_Slice($self->query, $self->analysis->logic_name); print STDOUT "Finished: Found ", scalar(@$db_features), " features already stored in the database\n"; print STDOUT "Finished: Found ", scalar(@$output), " features in the output\n"; my %db_feat = map { $self->get_feature_key($_), $_ } @$db_features; my %db_feat_to_del = %db_feat; ## remove old Uniprot features with missing sequence version.
if($self->analysis->logic_name eq 'Uniprot_raw') { foreach my $new_f (@$output) { $new_f->slice($self->query) if (!$new_f->slice); my $new_f_key = $self->get_feature_key($new_f,1); # get the string key without the sequence version
my $stored_f = $db_feat{$new_f_key}; if ($stored_f && $stored_f->display_id !~ /\.\d+/) { print STDOUT "Finished: Remove old Uniprot feature ".$stored_f->display_id. ", replaced by ".$new_f->display_id."\n"; $adaptor->remove($stored_f); delete $db_feat{$new_f_key} unless(!$db_feat{$new_f_key}); delete $db_feat_to_del{$new_f_key} unless(!$db_feat_to_del{$new_f_key}); } } } ## remove duplicated features from output
for (my $i = 0 ; $i < @$output ;) { my $feature = $output->[$i]; $feature->slice($self->query) if (!$feature->slice); my $f_key = $self->get_feature_key($feature); if ($db_feat{$f_key}) { splice(@$output, $i, 1); delete $db_feat_to_del{$f_key} unless(!$db_feat_to_del{$f_key}); } else { $i++; } } ## remove the old features present in the db and not in the output
if($all) { foreach my $f (values(%db_feat_to_del)) { $adaptor->remove($f);} print STDOUT "Finished: Removed ", scalar(keys(%db_feat_to_del)), " old features from db\n"; }
}
replace_outputdescriptionprevnextTop
sub replace_output {
  my ($self, @output) = @_;
  if(scalar(@output)){
  	$self->{'output'} = [];
    push(@{$self->{'output'}}, @output);
  }
  return $self->{'output'};
}
write_descriptionsdescriptionprevnextTop
sub write_descriptions {
    my( $self, $output ) = @_;
    my $dbobj = $self->db;
    my $type = $self->analysis->logic_name =~ /uniprot/i ? 'protein':'dna';
    my $seqfetcher = Bio::EnsEMBL::Pipeline::SeqFetcher::Finished_Dfetch->new(-type => $type, -analysis => $self->analysis);
    my %single_ids = map { $_->hseqname => 1} @$output;
    my @ids = keys(%single_ids);
    $seqfetcher->write_descriptions( $dbobj,\@ ids );
}
write_outputdescriptionprevnextTop
sub write_output {
	my ($self) = @_;
	my $outputs = $self->Bio::EnsEMBL::Analysis::RunnableDB::Finished::output;
    ### code db_version_searched method may be duplicated in several modules
### How does it get written into the input_id_analysis table?
foreach my $runnable ( @{ $self->runnable } ) { my $db_version = $runnable->get_db_version if $runnable->can('get_db_version'); $self->db_version_searched($db_version); # make sure we set this here
} my $dbh = $self->db->dbc->db_handle; $dbh->begin_work; eval { # We expect an array of arrays from output()
foreach my $output (@$outputs) { next unless @$output; # No feature output
my $feat = $output->[0]; my $is_align = ref($feat) =~ /AlignFeature$/ ? 1 : 0; # The type of adaptor used to store the data depends
# upon the type of the first element of @$output
my $adaptor = $self->get_adaptor($feat); # Remove the AlignFeatures already in db from the output and
# get rid of the old ones in the db (for dephtfilter features only)
my $all = 0; if ($is_align) { $all = 1 if($self->analysis->module =~ /DepthFilter/ ); $self->remove_stored_AlignFeatures($adaptor, $output, $all); $self->write_descriptions($output) unless ( $all || $self->analysis->logic_name =~ /refseq/); } else {# Remove all SimpleFeatures
$self->remove_all_features($adaptor); } my $analysis = $self->analysis; my $logic = $analysis->logic_name; my $slice = $self->query; my $ff = $self->feature_factory; foreach my $feature (@$output) { if($is_align){ my $hit_name = $feature->hseqname; $feature->external_db_id($self->get_extdb_id($logic,$hit_name)); } $feature->analysis($analysis); $feature->slice($slice) if (!$feature->slice); $ff->validate($feature); } if($adaptor->can('db_version')) { $adaptor->db_version($self->db_version_searched); } # Store features in the database
print STDOUT "Finished: Writing ".scalar(@$output)." new ".ref($feat)." in the database\n"; $adaptor->store(@$output) unless !@$output; } $dbh->commit; }; if ($@) { $dbh->rollback; throw("UNABLE TO WRITE FEATURES IN DATABASE\n[$@]\n"); }
}
General documentation
NAME - Bio::EnsEMBL::Analysis::RunnableDB::FinishedTop
AUTHORTop
Mustapha Larbaoui email ml6@sanger.ac.uk