Bio::Variation
SNP
Summary
Bio::Variation::SNP - submitted SNP
Package variables
Privates (from "my" definitions)
%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 => '', )
Included modules
Inherit
Synopsis
$SNP = Bio::Variation::SNP->new ();
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).
Methods
Methods description
Title : is_subsnp
Usage : $is = $snp->is_subsnp()
Function: returns 1 if $snp is a subSNP
Returns : 1 or undef
Args : NONE |
Title : subsnp
Usage : $subsnp = $snp->subsnp()
Function: returns the currently active subSNP of $snp
Returns : Bio::Variation::SNP
Args : NONE |
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 |
Title : each_subsnp
Usage : @subsnps = $snp->each_subsnp()
Function: returns a list of the subSNPs of a refSNP
Returns : list
Args : NONE |
Methods code
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};
}} | sub is_subsnp
{ return shift->{is_subsnp};} | sub subsnp
{ my $self = shift;
return $self->{subsnps}->[ scalar($self->each_subsnp) - 1 ];} | sub add_subsnp
{ my $self = shift;
$self->throw("add_subsnp(): cannot add subSNP to subSNP, only to refSNP")
if $self->is_subsnp;
my $subsnp = Bio::Variation::SNP->new;
push @{$self->{subsnps}}, $subsnp;
$self->subsnp->{is_subsnp} = 1;
return $self->subsnp;} | sub each_subsnp
{ my $self = shift;
$self->throw("each_subsnp(): cannot be called on a subSNP")
if $self->is_subsnp;
return @{$self->{subsnps}};} | General documentation
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
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/
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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