Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam
<![CDATA[
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::Runnable::Protein::Hmmpfam
=head1 SYNOPSIS
# something like this
my $query = new Bio::Seq(-file => $queryfile,
-format => 'Fasta');
my $hmm = Bio::EnsEMBL::Pipeline::Runnable::ProteinAnnotation::Pfam->new
('-query' => $query,
'-program' => 'hmmpfam' or '/usr/local/pubseq/bin/hmmpfam',
'-database' => '/data/Pfam_ls;/data/Pfam_fs');
$hmm->run;
my @results = @{$hmm->output};
=head1 DESCRIPTION
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Hmmpfam;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
sub multiprotein{
my ($self) = @_;
return 1;
}
##################################
sub run_analysis {
my ($self) = @_;
my @other_runnables;
foreach my $db_file (split(/;/, $self->analysis->db_file)) {
my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Hmmpfam->
new(-query => $self->query,
-analysis => $self->analysis,
-database => $db_file,
-options => $self->options);
$run->run;
push @other_runnables, $run;
}
$self->runnables_by_priority(\@other_runnables);
}
#################################
sub parse_results {
my ($self) = @_;
# the filter gets rid "secondary tier" hits (e.g. from
# fs matches) that overlap with "primary tier" matches.
my (%all_hits_by_seqid, @all_hits);
foreach my $run (@{$self->runnables_by_priority}) {
my %these_hits_by_seqid;
foreach my $hit (@{$run->output}) {
push @{$these_hits_by_seqid{$hit->seqname}}, $hit;
}
foreach my $seqid (keys %these_hits_by_seqid) {
my @kept_hits;
foreach my $hit (@{$these_hits_by_seqid{$seqid}}) {
my $overlap = 0;
if (exists($all_hits_by_seqid{$seqid})) {
foreach my $ohit (@{$all_hits_by_seqid{$seqid}}) {
if ($hit->start <= $ohit->end and $hit->end >= $ohit->start) {
$overlap = 1;
last;
}
}
}
if (not $overlap) {
push @kept_hits, $hit;
}
}
push @{$all_hits_by_seqid{$seqid}}, @kept_hits;
}
}
# finally, strip off those version numbers from the accessions
foreach my $seqid (keys %all_hits_by_seqid) {
foreach my $hit (@{$all_hits_by_seqid{$seqid}}) {
my $acc = $hit->hseqname;
$acc =~ s/\.\d+$//;
$hit->hseqname($acc);
push @all_hits, $hit;
}
}
$self->output(\@all_hits);
}
################################
sub runnables_by_priority {
my ($self, $runs) = @_;
if (defined $runs) {
$self->{_runs} = $runs;
}
return $self->{_runs};
}
1;
]]>