Bio/Variation/SNP.pm

   1 # bioperl module for Bio::Variation::SNP
   2 #
   3 # Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
   4 # Human Genetics, UCLA Medical School, University of California, Los Angeles
   5
   6 =head1 NAME
   7
   8 Bio::Variation::SNP - submitted SNP
   9
  10 =head1 SYNOPSIS
  11
  12   $SNP = Bio::Variation::SNP->new ();
  13
  14 =head1 DESCRIPTION
  15
  16 Inherits from Bio::Variation::SeqDiff and Bio::Variation::Allele, with
  17 additional methods that are (db)SNP specific (ie, refSNP/subSNP IDs, batch
  18 IDs, validation methods).
  19
  20 =head1 FEEDBACK
  21
  22 =head2 Mailing Lists
  23
  24 User feedback is an integral part of the evolution of this and other
  25 Bioperl modules. Send your comments and suggestions preferably to one
  26 of the Bioperl mailing lists. Your participation is much appreciated.
  27
  28   bioperl-l@bioperl.org                  - General discussion
  29   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  30
  31 =head2 Support
  32
  33 Please direct usage questions or support issues to the mailing list:
  34
  35 I<bioperl-l@bioperl.org>
  36
  37 rather than to the module maintainer directly. Many experienced and
  38 reponsive experts will be able look at the problem and quickly
  39 address it. Please include a thorough description of the problem
  40 with code and data examples if at all possible.
  41
  42 =head2 Reporting Bugs
  43
  44 Report bugs to the Bioperl bug tracking system to help us keep track
  45 the bugs and their resolution. Bug reports can be submitted via the
  46 web:
  47
  48   https://github.com/bioperl/bioperl-live/issues
  49
  50 =head1 AUTHOR
  51
  52 Allen Day E<lt>allenday@ucla.eduE<gt>
  53
  54 =head1 APPENDIX
  55
  56 The rest of the documentation details each of the object
  57 methods. Internal methods are usually preceded with a _
  58
  59 =cut
  60
  61 # Let the code begin...
  62
  63 package Bio::Variation::SNP;
  64
  65 use strict;
  66 use vars qw($AUTOLOAD);
  67 use Bio::Root::Root;
  68
  69 use base qw(Bio::Variation::SeqDiff Bio::Variation::Allele);
  70
  71 =head2 get/set-able methods
  72
  73  Usage   : $is = $snp->method()
  74  Function: for getting/setting attributes
  75  Returns : a value.  probably a scalar.
  76  Args    : if you're trying to set an attribute, pass in the new value.
  77
  78  Methods:
  79  --------
  80  id
  81  type
  82  observed
  83  seq_5
  84  seq_3
  85  ncbi_build
  86  ncbi_chr_hits
  87  ncbi_ctg_hits
  88  ncbi_seq_loc
  89  ucsc_build
  90  ucsc_chr_hits
  91  ucsc_ctg_hits
  92  heterozygous
  93  heterozygous_SE
  94  validated
  95  genotype
  96  handle
  97  batch_id
  98  method
  99  locus_id
 100  symbol
 101  mrna
 102  protein
 103  functional_class
 104
 105 =cut
 106
 107 #'
 108 my %OK_AUTOLOAD = (
 109                 id                      => '',
 110                 type                    => '',
 111                 observed                => [],
 112                 seq_5                   => '',
 113                 seq_3                   => '',
 114                 ncbi_build              => '',
 115                 ncbi_chr_hits           => '',
 116                 ncbi_ctg_hits           => '',
 117                 ncbi_seq_loc            => '',
 118                 ucsc_build              => '',
 119                 ucsc_chr_hits           => '',
 120                 ucsc_ctg_hits           => '',
 121                 heterozygous            => '',
 122                 heterozygous_SE         => '',
 123                 validated               => '',
 124                 genotype                => '',
 125                 handle                  => '',
 126                 batch_id                => '',
 127                 method                  => '',
 128                 locus_id                => '',
 129                 symbol                  => '',
 130                 mrna                    => '',
 131                 protein                 => '',
 132                 functional_class        => '',
 133                 );
 134
 135 sub AUTOLOAD {
 136         my $self = shift;
 137         my $param = $AUTOLOAD;
 138         $param =~ s/.*:://;
 139         $self->throw(__PACKAGE__." doesn't implement $param") unless defined $OK_AUTOLOAD{$param};
 140
 141         if( ref $OK_AUTOLOAD{$param} eq 'ARRAY' ) {
 142                 push @{$self->{$param}}, shift if @_;
 143                 return $self->{$param}->[scalar(@{$self->{$param}}) - 1];
 144         } else {
 145                 $self->{$param} = shift if @_;
 146                 return $self->{$param};
 147         }
 148 }
 149
 150
 151 #foreach my $slot (keys %RWSLOT){
 152 #       no strict "refs"; #add class methods to package
 153 #       *$slot = sub {
 154 #               shift;
 155 #               $RWSLOT{$slot} = shift if @_;
 156 #               return $RWSLOT{$slot};
 157 #       };
 158 #}
 159
 160
 161 =head2 is_subsnp
 162
 163  Title   : is_subsnp
 164  Usage   : $is = $snp->is_subsnp()
 165  Function: returns 1 if $snp is a subSNP
 166  Returns : 1 or undef
 167  Args    : NONE
 168
 169 =cut
 170
 171 sub is_subsnp {
 172         return shift->{is_subsnp};
 173 }
 174
 175 =head2 subsnp
 176
 177  Title   : subsnp
 178  Usage   : $subsnp = $snp->subsnp()
 179  Function: returns the currently active subSNP of $snp
 180  Returns : Bio::Variation::SNP
 181  Args    : NONE
 182
 183 =cut
 184
 185 sub subsnp {
 186         my $self = shift;
 187         return $self->{subsnps}->[ scalar($self->each_subsnp) - 1 ];
 188 }
 189
 190 =head2 add_subsnp
 191
 192  Title   : add_subsnp
 193  Usage   : $subsnp = $snp->add_subsnp()
 194  Function: pushes the previous value returned by subsnp() onto a stack,
 195            accessible with each_subsnp().
 196            Sets return value of subsnp() to a new Bio::Variation::SNP
 197            object, and returns that object.
 198  Returns : Bio::Varitiation::SNP
 199  Args    : NONE
 200
 201 =cut
 202
 203 sub add_subsnp {
 204         my $self = shift;
 205         $self->throw("add_subsnp(): cannot add subSNP to subSNP, only to refSNP")
 206             if $self->is_subsnp;
 207
 208         my $subsnp = Bio::Variation::SNP->new;
 209         push @{$self->{subsnps}}, $subsnp;
 210         $self->subsnp->{is_subsnp} = 1;
 211         return $self->subsnp;
 212 }
 213
 214 =head2 each_subsnp
 215
 216  Title   : each_subsnp
 217  Usage   : @subsnps = $snp->each_subsnp()
 218  Function: returns a list of the subSNPs of a refSNP
 219  Returns : list
 220  Args    : NONE
 221
 222 =cut
 223
 224 sub each_subsnp {
 225         my $self = shift;
 226         $self->throw("each_subsnp(): cannot be called on a subSNP")
 227             if $self->is_subsnp;
 228         return @{$self->{subsnps}};
 229 }
 230
 231 1;