Bio::PopGen TagHaplotype
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Summary
Bio::PopGen::TagHaplotype.pm - Haplotype tag object.
Package variables
Privates (from "my" definitions)
$USAGE = <<EOFUsage: Bio::PopGen::TagHaplotype->new(-haplotype_block =>\$ hapblockref)EOF
Included modules
Data::Dumper
Storable qw ( dclone )
Inherit
Bio::Root::Root
Synopsis
    use Bio::PopGen::TagHaplotype;
my $obj = Bio::PopGen::TagHaplotype -> new($hap);
Description
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 Select.mp
module also on this folder. In any case if, you provide an haplotype
the module will try to find the answer to your question.
Methods
newDescriptionCode
haplotype_blockDescriptionCode
input_blockDescriptionCode
tag_listDescriptionCode
tag_lengthDescriptionCode
_scan_snpDescriptionCode
_gen_combDescriptionCode
_generateCombinationsDescriptionCode
_scan_combinationsDescriptionCode
_deg_test
No description
Code
_get_subArray
No description
Code
compare_arrays
No description
Code
Methods description
newcode    nextTop
 Title   : new
Function: constructor of the class.
Returns : self hash
Args : input haplotype (array of array)
Status : public
haplotype_blockcodeprevnextTop
 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
tag_listcodeprevnextTop
 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 : $obj->tag_length()
Function: returns the length of the tag.
Returns : scalar
Args : none
Status : public
_scan_snp codeprevnextTop
 Title   : _scan_snp 
Usage : internal
Function: scan sets increasing the length until find a non degenerated
pattern.
Returns : scalar
Args : none
Status : private
_gen_combcodeprevnextTop
 Title   : _gen_comb 
Usage : internal
Function: we supply the length of the haplotype and the length of the
word we need to find and the functions returns the possible
list of combinations.
Returns : scalar
Args : none
Status : private
_generateCombinations codeprevnextTop
 Title   : _generateCombinations 
Usage : internal
Function: Recursive function that produce all combinations for a set
i.e.: 1, 2, 3, 4 and word of 3 will produce:
1, 2, 3 1, 2, 4 1, 3, 4 2, 3, 4 Returns : Args : none Status : private
_scan_combinations codeprevnextTop
 Title   : _scan_combinations 
Usage : internal
Function: take the haplotype and a list of possible combination
for that length. Generate a subset and scan it to find if
the information is enought to define the haplotype set.
Returns :
Args : none
Status : private
Methods code
newdescriptionprevnextTop
sub new {
#------------------------
my ($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 $self;
}
haplotype_blockdescriptionprevnextTop
sub haplotype_block {
    my ($self) =shift;
    return $self->{'_haplotype_block'} = shift if @_;
    return $self->{'_haplotype_block'};
}
input_blockdescriptionprevnextTop
sub input_block {
#------------------------
my $self = shift; $self->warn(ref($self). "::input_block - deprecated method. Use haplotype_block() instead."); return $self->haplotype_block;
}
tag_listdescriptionprevnextTop
sub tag_list {
#------------------------
my ($self) = shift; return $self->{'_tag_list'}= shift if @_; return $self->{'_tag_list'};
}
tag_lengthdescriptionprevnextTop
sub tag_length {
#------------------------
my ($self) =shift; return $self ->{'_tag_length'} = shift if @_; return $self ->{'_tag_length'};
}
_scan_snpdescriptionprevnextTop
sub _scan_snp {
#------------------------
my ($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 $snp_collection; } }
}
_gen_combdescriptionprevnextTop
sub _gen_comb {
#------------------------
my ($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 $list;
}
_generateCombinationsdescriptionprevnextTop
sub _generateCombinations {
#------------------------
my ($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)
#
}
_scan_combinationsdescriptionprevnextTop
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 $valid_combination; } # return 1 if two arrays are degenerated (same haplotype)
#------------------------
}
_deg_testdescriptionprevnextTop
sub _deg_test {
#------------------------
my ($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 ($degeneration){ # if the two arrays are the same
return 1; } } } } #------------------------
}
_get_subArraydescriptionprevnextTop
sub _get_subArray {
#------------------------
my($hap, $combination) =@_; my $out = []; # output array to be tested
for my $i (0..$#$hap){ foreach(@$combination){ push @{$out->[$i]}, $hap->[$i][$_]; } } return $out; } #
# take two arrays and compare their values
# Returns : 1 if the two values are the same
# 0 if the values are different
#
#------------------------
}
compare_arraysdescriptionprevnextTop
sub compare_arrays {
#------------------------
my ($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
CONSTRUCTORSTop
    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] ];
FEEDBACKTop
Mailing ListsTop
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 list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Pedro M. Gomez-FabreTop
Email pgf18872-at-gsk-dot-com