Raw content of Bio::EnsEMBL::Compara::Subset
<![CDATA[# $Id: Subset.pm,v 1.5 2005/07/14 15:05:39 jh7 Exp $
#
# Module to handle family members
#
# Cared for by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright Abel Ureta-Vidal
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Subset - DESCRIPTION of Object
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
Jessica Severin <jessica@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Subset;
use strict;
use Bio::Species;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Argument;
sub new {
my ($class, @args) = @_;
my $self = {};
bless $self,$class;
if (scalar @args) {
#do this explicitly.
my ($dbid, $description, $adaptor) = rearrange([qw(DBID NAME ADAPTOR)], @args);
$self->dbID($dbid) if($dbid);
$self->description($description) if($description);
$self->adaptor($adaptor) if($adaptor);
$self->{'_member_id_list'} = [];
$self->{'_cached_member_list'} = [];
}
return $self;
}
=head2 new_fast
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype :
Exceptions : none
Caller :
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 adaptor
Title : adaptor
Usage :
Function: give the adaptor if known
Example :
Returns :
Args :
=cut
sub adaptor {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_adaptor'} = $value;
}
return $self->{'_adaptor'};
}
=head2 dbID
Arg [1] : int $dbID (optional)
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub dbID {
my $self = shift;
$self->{'_dbID'} = shift if(@_);
return $self->{'_dbID'};
}
=head2 description
Arg [1] : string $description (optional)
Example :
Description:
Returntype : string
Exceptions :
Caller :
=cut
sub description {
my $self = shift;
$self->{'_description'} = shift if(@_);
return $self->{'_description'};
}
=head2 dump_loc
Arg [1] : string $dump_loc (optional)
Example :
Description:
Returntype : string
Exceptions :
Caller :
=cut
sub dump_loc {
my $self = shift;
$self->{'_dump_loc'} = shift if(@_);
return $self->{'_dump_loc'};
}
=head2 add_member_id
Arg [1] : $member_id
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub add_member_id {
my $self = shift;
my $count=0;
if(@_) {
my $member_id = shift;
$count = push @{$self->{'_member_id_list'}}, $member_id;
#print("added $count element to list\n");
if(defined($self->adaptor)) {
$self->adaptor->store_link($self, $member_id);
}
}
return $count
}
sub add_member {
my ($self, $member) = @_;
unless(defined($member) and $member->isa('Bio::EnsEMBL::Compara::Member')) {
throw(
"gene arg must be a [Bio::EnsEMBL::Compara::Member] ".
"not a [$member]");
}
my $count = $self->add_member_id($member->dbID);
push @{$self->{'_cached_member_list'}}, $member;
return $count;
}
=head2 member_list
Arg [1] :
Example :
Description:
Returntype : reference to array of Bio::EnsEMBL::Compara::Member objects
Exceptions :
Caller :
=cut
sub member_id_list {
my $self = shift;
return $self->{'_member_id_list'};
}
sub member_list {
my $self = shift;
return $self->{'_cached_member_list'};
}
sub count {
my $self = shift;
return $#{$self->member_id_list()} + 1;
#return $#{$self->member_list()} + 1;
#my @idList = @{$self->member_id_list()};
#my $count = $#idList;
#return $count;
}
sub output_to_fasta {
my ($self, $fastaPath, $prefix) = @_;
if(defined($fastaPath)) {
if($fastaPath ne "stdout") {
open FASTA_FP,">$fastaPath";
} else {
open FASTA_FP,">-";
}
}
foreach my $member (@{member_list()}) {
my $seq_string = $member->sequence;
$seq_string =~ s/(.{72})/$1\n/g;
print FASTA_FP ">$prefix" .
$member->stable_id . " " .
$member->description . "\n" .
$seq_string . "\n";
}
close(FASTA_FP);
}
1;
]]>