Bio::PopGen TagHaplotype
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary - Haplotype tag object.
Package variables
Privates (from "my" definitions)
$USAGE = <<EOFUsage: Bio::PopGen::TagHaplotype->new(-haplotype_block =>\$ hapblockref)EOF
Included modules
Storable qw ( dclone )
    use Bio::PopGen::TagHaplotype;
my $obj = Bio::PopGen::TagHaplotype -> new($hap);
This module take as input a haplotype and try toe get the minimal set
of SNP that define the haplotype. This module can be use alone. But
due to the tagging haplotype process is exponential one. My suggestion
is that before to use this module you pass your data under
module also on this folder. In any case if, you provide an haplotype
the module will try to find the answer to your question.
No description
No description
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Methods description
newcode    nextTop
 Title   : new
Function: constructor of the class.
Returns : self hash
Args : input haplotype (array of array)
Status : public
 Title   : haplotype_block
Usage : my $haplotype_block = $TagHaplotype->haplotype_block();
Function: Get the haplotype block for a haplotype tagging selection
Returns : reference of array
Args : reference of array with haplotype pattern
input_block codeprevnextTop
 Title   : input_block 
Usage : $obj->input_block()
Function: returns haplotype block. By now will produce the same output than
$self->haplotype_block. but for compatiblity, this method is kept.
This method is deprecated.
Returns : reference to array of array with the haplotype input value
Args : none
Status : public
 Title   : tag_list 
Usage : $obj->tag_list()
Function: returns the list of SNPs combination that identify the
haplotype. All combinations are displayed as arrays
Returns : reference to array of array.
Args : none
Status : public
tag_length codeprevnextTop
 Title   : tag_length 
Usage : $obj->tag_length()
Function: returns the length of the tag.
Returns : scalar
Args : none
Status : public
_scan_snp codeprevnextTop
 Title   : _scan_snp 
Usage : internal
Function: scan sets increasing the length until find a non degenerated
Returns : scalar
Args : none
Status : private
 Title   : _gen_comb 
Usage : internal
Function: we supply the length of the haplotype and the length of the
word we need to find and the functions returns the possible
list of combinations.
Returns : scalar
Args : none
Status : private
_generateCombinations codeprevnextTop
 Title   : _generateCombinations 
Usage : internal
Function: Recursive function that produce all combinations for a set
i.e.: 1, 2, 3, 4 and word of 3 will produce:
1, 2, 3 1, 2, 4 1, 3, 4 2, 3, 4 Returns : Args : none Status : private
_scan_combinations codeprevnextTop
 Title   : _scan_combinations 
Usage : internal
Function: take the haplotype and a list of possible combination
for that length. Generate a subset and scan it to find if
the information is enought to define the haplotype set.
Returns :
Args : none
Status : private
Methods code
sub new {
my ($class, @args) = @_; my $self = $class->SUPER::new(@args); my ($haplotype_block) = $self->_rearrange([qw(HAPLOTYPE_BLOCK)],@args); if ($haplotype_block) { $self->haplotype_block($haplotype_block); } else{ $self->throw("haplotype has not been supplied\n$USAGE"); } # check that the haplotype block is well formed.
for (my $i=0; $i<$#$haplotype_block+1; $i++){ if ( $#{$haplotype_block->[0]} != $#{$haplotype_block->[$i]} ){ $self->throw("The haplotype matrix is not well formed (Not squared)"); } } # make the calculation
my $tag_list = _scan_snp( $self ->haplotype_block ); if ($tag_list){ $self ->tag_list($tag_list); } else { $self ->tag_list(undef); } if ( defined $self->tag_list){ $self ->tag_length(scalar @{$self->tag_list}); } else { $self ->tag_length(0); #"NO TAGS FOUND!"
} return $self;
sub haplotype_block {
    my ($self) =shift;
    return $self->{'_haplotype_block'} = shift if @_;
    return $self->{'_haplotype_block'};
sub input_block {
my $self = shift; $self->warn(ref($self). "::input_block - deprecated method. Use haplotype_block() instead."); return $self->haplotype_block;
sub tag_list {
my ($self) = shift; return $self->{'_tag_list'}= shift if @_; return $self->{'_tag_list'};
sub tag_length {
my ($self) =shift; return $self ->{'_tag_length'} = shift if @_; return $self ->{'_tag_length'};
sub _scan_snp {
my ($hap)=@_; my $hap_length = scalar @{$hap->[0]}; ## store the haplotype length
for my $i(1..$hap_length){ my $list = _gen_comb($hap_length, $i); my $snp_collection = _scan_combinations($hap, $list); # if there is any element on the collection.
# We have reached our goal and
# we can stop the calculation.
if($#$snp_collection>-1){ return $snp_collection; } }
sub _gen_comb {
my ($hap_length,$n) = @_; my @array = (); # list with all elements we have to combine
for(0..$hap_length-1){ push @array, $_ }; #
# we need some parameters to create the combination list.
# This parameters can be changed if we can modify the list values
my $m = -1; # this parameter start the calculation at value
# m+1 on the recursive cicle.
my $value = []; ## seems to have not too much sense here, but is
## needed on the recursion and need to be started
## from here
my $list = []; _generateCombinations (\@ array,\$ m, \$n, $value, $list);
return $list;
sub _generateCombinations {
my ($rarr, $rm, $rn, $rvalue,$rlist)=@_; for (my $i = ($$rm+1); $i<scalar @$rarr; $i++){ push (my @value2,@$rvalue,$rarr->[$i]); if (scalar @value2<$$rn){ _generateCombinations($rarr,\$i, $rn,\@ value2, $rlist); } if (scalar @value2==$$rn){ push @$rlist, [@value2]; } if(scalar @value2>$$rn){ last; } } } # take the list of combinations
# i.e.: 1 2 3
# 1 2 4
# 1 3 4
# 2 3 4
# generate a sub array from the haplotype with the snp tag for the combination
# and check all haplotypes for these columns.
# if two haplotypes have the same value. we can not define the haplotype
# without ambiguity.
# Will return a list of valid combinations (SNP Tags)
sub _scan_combinations {
my($hap,$list) = @_; my $valid_combination = undef; # we have to check every snp combinations from the list
for my $i (0..$#$list){ # extract from the big array the one we will use for tag calculations
my $subArray = _get_subArray ($hap, $list->[$i]); my $degeneration = _deg_test($subArray); if(!$degeneration){ push @$valid_combination, [@{$list->[$i]}]; } } return $valid_combination; } # return 1 if two arrays are degenerated (same haplotype)
sub _deg_test {
my ($hap)= @_; # for every sub array we compare each element with the rest
for my $c1(0..$#$hap){ for my $c2($c1+1..$#$hap){ my $degeneration = compare_arrays($hap->[$c1], $hap->[$c2]); if ($degeneration){ # if the two arrays are the same
return 1; } } } } #------------------------
sub _get_subArray {
my($hap, $combination) =@_; my $out = []; # output array to be tested
for my $i (0..$#$hap){ foreach(@$combination){ push @{$out->[$i]}, $hap->[$i][$_]; } } return $out; } #
# take two arrays and compare their values
# Returns : 1 if the two values are the same
# 0 if the values are different
sub compare_arrays {
my ($first, $second) = @_; return 0 unless @$first == @$second; for (my $i = 0; $i < @$first; $i++) { return 0 if $first->[$i] ne $second->[$i]; } return 1; } 1;
General documentation
    my $obj = Bio::PopGen::TagHaplotype -> new($hap);
were $hap is the reference to an array of array with the haplotype. $hap= [[0, 0, 0], [1, 0, 0], [0, 1, 1] ];
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AUTHOR - Pedro M. Gomez-FabreTop
Email pgf18872-at-gsk-dot-com