Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Finished::Exonerate
<![CDATA[### Bio::EnsEMBL::Analysis::RunnableDB::Finished::Exonerate
package Bio::EnsEMBL::Analysis::RunnableDB::Finished::Exonerate;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning);
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Exon;
use Bio::EnsEMBL::DnaDnaAlignFeature;
use Bio::EnsEMBL::DnaPepAlignFeature;
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Analysis::Runnable::Finished::Exonerate;
use Bio::EnsEMBL::Pipeline::SeqFetcher::Finished_Pfetch;
use Bio::EnsEMBL::Analysis::Config::General;
use base 'Bio::EnsEMBL::Analysis::RunnableDB::Finished';
############################################################
sub fetch_input {
my ($self) = @_;
my $slice =
$self->fetch_sequence( $self->input_id, $self->db,
$ANALYSIS_REPEAT_MASKING, 1 );
$self->query($slice);
my $maskedslice =
$slice->get_repeatmasked_seq( $ANALYSIS_REPEAT_MASKING, $SOFT_MASKING )
or throw("Unable to fetch contig");
my $maskedseq = $maskedslice->seq();
if ( scalar( $maskedseq =~ s/([CATG])/$1/g ) > 3 ) {
$self->input_is_void(0);
}
else {
$self->input_is_void(1);
warning("Need at least 3 nucleotides");
}
# Incremental updating of the embl blast db analysis
# The embl blast dbs are made up of release files embl_*
# and update files emnew_*. This block of code makes
# sure that the analysis is only run against new version of either
# of these files.
my @files = split(",", $self->analysis->db_file);
my @patches;
if($files[-1] =~ /^embl_/){
my $search_only_patch = 0;
my $sic = $self->db->get_StateInfoContainer;
my $db_version_saved = $sic->fetch_db_version($self->input_id, $self->analysis);
my $db_version_current = $self->analysis->db_version;
if($db_version_saved) {
# split the embl blast db version "12-Mar-06 (85)" to
# patch version "12-Mar-06" and release version "85"
my ($patch_sv,$release_sv) = $db_version_saved =~ /^(\S+)\s+\((\d+)\)$/;
my ($patch_cv,$release_cv) = $db_version_current =~ /^(\S+)\s+\((\d+)\)$/;
if($release_sv eq $release_cv){
$search_only_patch = 1;
print STDOUT "blast db files [ @files ] version $release_sv already searched\n";
# Just to make sure that nothing is going wrong with the incremental updating...
throw("Problem with the embl blast db incremental updating, saved and current version identical !\n
saved [$db_version_saved] = current [$db_version_current]\n") unless($patch_sv ne $patch_cv)
}
}
foreach my $file (@files) {
my $patch_file = $file;
$patch_file =~ s/^embl_/emnew_/g;
$search_only_patch ? $file = $patch_file : push @patches,$patch_file;
}
}
$self->analysis->db_file(join(",",@files,@patches));
my %parameters = %{ $self->parameters_hash };
my $runnable = Bio::EnsEMBL::Analysis::Runnable::Finished::Exonerate->new(
-analysis => $self->analysis,
-program => $self->analysis->program,
-query_db => $self->analysis->db_file,
-target => $slice,
%parameters
);
$self->runnable($runnable);
return 1;
}
sub db_version_searched {
my ( $self, $arg ) = @_;
$self->{'_db_version_searched'} = $arg if $arg;
return $self->{'_db_version_searched'};
}
1;
=head1 NAME - Bio::EnsEMBL::Analysis::RunnableDB::Finished::Exonerate
=head1 AUTHOR
Mustapha Larbaoui B<email> ml6@sanger.ac.uk
]]>