Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Finished
<![CDATA[### Bio::EnsEMBL::Analysis::RunnableDB::Finished
package Bio::EnsEMBL::Analysis::RunnableDB::Finished;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning);
use Bio::EnsEMBL::Pipeline::SeqFetcher::Finished_Dfetch;
use base 'Bio::EnsEMBL::Analysis::RunnableDB';
my %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 }
);
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 $logic_name\n");
}
sub write_output {
my ($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");
}
}
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 $self->{'output'};
}
sub replace_output {
my ($self, @output) = @_;
if(scalar(@output)){
$self->{'output'} = [];
push(@{$self->{'output'}}, @output);
}
return $self->{'output'};
}
sub remove_stored_AlignFeatures {
my ($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";
}
}
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";
}
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 );
}
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, $feat->hend );
}
sub get_adaptor {
my ($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;
=head1 NAME - Bio::EnsEMBL::Analysis::RunnableDB::Finished
=head1 AUTHOR
Mustapha Larbaoui B<email> ml6@sanger.ac.uk
]]>