Raw content of Bio::Variation::SNP
<![CDATA[# $Id: SNP.pm,v 1.9 2002/10/22 07:38:49 lapp Exp $
# bioperl module for Bio::Variation::SNP
#
# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
# Human Genetics, UCLA Medical School, University of California, Los Angeles
=head1 NAME
Bio::Variation::SNP - submitted SNP
=head1 SYNOPSIS
$SNP = Bio::Variation::SNP->new ();
=head1 DESCRIPTION
Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with
additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch
IDs, validation methods).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Allen Day E<lt>allenday@ucla.eduE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Variation::SNP;
my $VERSION=1.0;
use strict;
use vars qw($VERSION @ISA $AUTOLOAD);
use Bio::Root::Root;
use Bio::Variation::SeqDiff;
use Bio::Variation::Allele;
@ISA = qw( Bio::Variation::SeqDiff Bio::Variation::Allele);
=head2 get/set-able methods
Usage : $is = $snp->method()
Function: for getting/setting attributes
Returns : a value. probably a scalar.
Args : if you're trying to set an attribute, pass in the new value.
Methods:
--------
id
type
observed
seq_5
seq_3
ncbi_build
ncbi_chr_hits
ncbi_ctg_hits
ncbi_seq_loc
ucsc_build
ucsc_chr_hits
ucsc_ctg_hits
heterozygous
heterozygous_SE
validated
genotype
handle
batch_id
method
locus_id
symbol
mrna
protein
functional_class
=cut
my %OK_AUTOLOAD = (
id => '',
type => '',
observed => [],
seq_5 => '',
seq_3 => '',
ncbi_build => '',
ncbi_chr_hits => '',
ncbi_ctg_hits => '',
ncbi_seq_loc => '',
ucsc_build => '',
ucsc_chr_hits => '',
ucsc_ctg_hits => '',
heterozygous => '',
heterozygous_SE => '',
validated => '',
genotype => '',
handle => '',
batch_id => '',
method => '',
locus_id => '',
symbol => '',
mrna => '',
protein => '',
functional_class => '',
);
sub AUTOLOAD {
my $self = shift;
my $param = $AUTOLOAD;
$param =~ s/.*:://;
$self->throw(__PACKAGE__." doesn't implement $param") unless defined $OK_AUTOLOAD{$param};
if( ref $OK_AUTOLOAD{$param} eq 'ARRAY' ) {
push @{$self->{$param}}, shift if @_;
return $self->{$param}->[scalar(@{$self->{$param}}) - 1];
} else {
$self->{$param} = shift if @_;
return $self->{$param};
}
}
#foreach my $slot (keys %RWSLOT){
# no strict "refs"; #add class methods to package
# *$slot = sub {
# shift;
# $RWSLOT{$slot} = shift if @_;
# return $RWSLOT{$slot};
# };
#}
=head2 is_subsnp
Title : is_subsnp
Usage : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args : NONE
=cut
sub is_subsnp {
return shift->{is_subsnp};
}
=head2 subsnp
Title : subsnp
Usage : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args : NONE
=cut
sub subsnp {
my $self = shift;
return $self->{subsnps}->[ scalar($self->each_subsnp) - 1 ];
}
=head2 add_subsnp
Title : add_subsnp
Usage : $subsnp = $snp->add_subsnp()
Function: pushes the previous value returned by subsnp() onto a stack, accessible with each_subsnp().
sets return value of subsnp() to a new Bio::Variation::SNP object, and returns that object.
Returns : Bio::Varitiation::SNP
Args : NONE
=cut
sub add_subsnp {
my $self = shift;
$self->throw("add_subsnp(): cannot add sunSNP to subSNP, only refSNP") if $self->is_subsnp;
my $subsnp = Bio::Variation::SNP->new;
push @{$self->{subsnps}}, $subsnp;
$self->subsnp->{is_subsnp} = 1;
return $self->subsnp;
}
=head2 each_subsnp
Title : each_subsnp
Usage : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args : NONE
=cut
sub each_subsnp {
my $self = shift;
$self->throw("each_subsnp(): cannot be called on a subSNP") if $self->is_subsnp;
return @{$self->{subsnps}};
}
1;
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