Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene2x
<![CDATA[# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene2x.pm
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene_DB->new(
-db => $db_adaptor,
-input_id => $slice_id,
-analysis => $analysis,
);
$runnabledb->fetch_input();
$runnabledb->run();
my @array = @{$runnabledb->output};
$runnabledb->write_output();
=head1 DESCRIPTION
This object wraps Bio::EnsEMBL::Analysis::Runnable::Pseudogene2x.pm
Specidfic behaviour for Pseudogene identification in 2x gene-builds
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene2x;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::Analysis::Config::Pseudogene;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning
stack_trace);
use Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene_DB;
use Bio::EnsEMBL::Analysis::Runnable::Pseudogene2x;
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Pseudogene_DB );
sub fetch_input {
my( $self) = @_;
$self->SUPER::fetch_input;
my $genes_slice = $self->query;
my @seq_level_features;
foreach my $bit (@{$genes_slice->project('seqlevel')}) {
push @seq_level_features, Bio::EnsEMBL::Feature->new(-start => $bit->from_start + $genes_slice->start - 1,
-end => $bit->from_end + $genes_slice->start - 1,
-strand => 1);
}
foreach my $run (@{$self->runnable}) {
$run->seqlevel(\@seq_level_features);
}
}
sub make_runnable {
my ($self) = @_;
my $run = Bio::EnsEMBL::Analysis::Runnable::Pseudogene2x->new
(
-analysis => $self->analysis,
-genes => $self->genes,
-repeat_features => $self->repeat_blocks,
-PS_REPEAT_TYPES => $self->PS_REPEAT_TYPES,
-PS_FRAMESHIFT_INTRON_LENGTH => $self->PS_FRAMESHIFT_INTRON_LENGTH,
-PS_MAX_INTRON_LENGTH => $self->PS_MAX_INTRON_LENGTH,
-PS_MAX_INTRON_COVERAGE => $self->PS_MAX_INTRON_COVERAGE,
-PS_MAX_EXON_COVERAGE => $self->PS_MAX_EXON_COVERAGE,
-PS_NUM_FRAMESHIFT_INTRONS => $self->PS_NUM_FRAMESHIFT_INTRONS,
-PS_NUM_REAL_INTRONS => $self->PS_NUM_REAL_INTRONS,
-SINGLE_EXON => $self->SINGLE_EXON,
-INDETERMINATE => $self->INDETERMINATE,
-PS_MIN_EXONS => $self->PS_MIN_EXONS,
-PS_MULTI_EXON_DIR => $self->PS_MULTI_EXON_DIR,
-BLESSED_BIOTYPES => $self->BLESSED_BIOTYPES,
-PS_PSEUDO_TYPE => $self->PS_PSEUDO_TYPE,
-PS_BIOTYPE => $self->PS_BIOTYPE,
-PS_REPEAT_TYPE => $self->PS_REPEAT_TYPE,
-DEBUG => $self->DEBUG,
);
$self->runnable($run);
}
sub get_all_repeat_blocks {
my ($self,$repeat_ref) = @_;
my @repeat_blocks;
my @repeats = @{$repeat_ref};
@repeats = sort {$a->start <=> $b->start} @repeats;
my $curblock = undef;
REPLOOP: foreach my $repeat (@repeats) {
my $rc = $repeat->repeat_consensus;
if ($rc->repeat_class !~ /LINE/ &&
$rc->repeat_class !~ /LTR/ &&
$rc->repeat_class !~ /SINE/ &&
$rc->repeat_class !~ /Unknown/) {
next REPLOOP;
}
if ($repeat->start <= 0) {
$repeat->start(1);
}
if (defined($curblock) && $curblock->end >= $repeat->start) {
if ($repeat->end > $curblock->end) {
$curblock->end($repeat->end);
}
} else {
$curblock = Bio::EnsEMBL::Feature->new(
-START => $repeat->start,
-END => $repeat->end,
-STRAND => $repeat->strand
);
push (@repeat_blocks,$curblock);
}
}
@repeat_blocks = sort {$a->start <=> $b->start} @repeat_blocks;
return\@repeat_blocks;
}
1;
]]>