Bio::Matrix
PhylipDist
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Summary
Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Matrix::PhylipDist;
my $dist = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",-program=>"ProtDist");
#or
my $dist = Bio::Matrix::PhylipDist->new(-fh=>$FH,-program=>"ProtDist");
#get specific entries
my $distance_value = $dist->get_entry('ALPHA','BETA');
my @columns = $dist->get_column('ALPHA');
my @rows = $dist->get_row('BETA');
my @diagonal = $dist->get_diagonal();
#print the matrix in phylip numerical format
print $dist->print_matrix;
Description
Simple object for holding Distance Matrices generated by the following Phylip programs:
1) dnadist
2) protdist
3) restdist
It currently handles parsing of the matrix without the data output option.
5
Alpha 0.00000 4.23419 3.63330 6.20865 3.45431
Beta 4.23419 0.00000 3.49289 3.36540 4.29179
Gamma 3.63330 3.49289 0.00000 3.68733 5.84929
Delta 6.20865 3.36540 3.68733 0.00000 4.43345
Epsilon 3.45431 4.29179 5.84929 4.43345 0.00000
Methods
Methods description
Title : _matrix
Usage : $matrix->_matrix();
Function: get/set for hash reference of the pointers
to the value matrix
Returns : hash reference
Arguments: hash reference |
Title : _parse
Usage : $matrix->_parse();
Function: internal method that parses the distance matrix file.
Returns :
Arguments: |
Title : _values
Usage : $matrix->_values();
Function: get/set for array ref of the matrix containing
distance values
Returns : an array reference
Arguments: an array reference |
Title : get_column
Usage : $matrix->get_column('ALPHA');
Function: returns a particular column
Returns : an array of floats
Arguments: string id1 |
Title : get_diagonal
Usage : $matrix->get_diagonal();
Function: returns the diagonal of the matrix
Returns : an array of float
Arguments: string id1 |
Title : get_entry
Usage : $matrix->get_entry();
Function: returns a particular entry
Returns : a float
Arguments: string id1, string id2 |
Title : get_row
Usage : $matrix->get_row('ALPHA');
Function: returns a particular row
Returns : an array of float
Arguments: string id1 |
Title : names
Usage : $matrix->names();
Function: get/set for array ref of names of sequences
Returns : an array reference
Arguments: an array reference |
Title : new
Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
-program=>"protdist");
Function: Constructor for PhylipDist Object
Returns : Bio::Matrix::PhylipDist |
Title : print_matrix
Usage : $matrix->print_matrix();
Function: returns a string of the matrix in phylip format
Returns : a string
Arguments: |
Title : program
Usage : $matrix->program();
Function: get/set for the program name generating this
matrix
Returns : string
Arguments: string |
Methods code
sub _matrix
{ my ($self,$val) = @_;
if($val){
$self->{'_matrix'} = $val;
}
return $self->{'_matrix'};} | sub _parse
{ my ($self) = @_;
my @names;
my @values;
while (my $entry = $self->_readline){
next if ($entry=~/^\s+\d+$/);
my ($n,@line) = split( /\s+/,$entry);
push @names, $n;
push @values, [@line];
}
my %dist;
my $i=0;
foreach my $name(@names){
my $j=0;
foreach my $n(@names) {
$dist{$name}{$n} = [$i,$j];
$j++;
}
$i++;
}
$self->_matrix(\%dist);
$self->names(\@names);
$self->_values(\@values);} | sub _values
{ my ($self,$val) = @_;
if($val){
$self->{'_values'} = $val;
}
return $self->{'_values'};
}
1;} | sub get_column
{ my ($self,$column) = @_;
$column || $self->throw("Need at least a column id");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @names = @{$self->names};
$matrix{$column} || return;
my @column = %{$matrix{$column}};
my $row_pointer = $column[1]->[0];
my @return;
for(my $i=0; $i < scalar(@names); $i++){
push @return, $values[$i][$row_pointer];
}
return @return;} | sub get_diagonal
{ my ($self) = @_;
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @return;
foreach my $name (@{$self->names}){
my ($i,$j) = @{$matrix{$name}{$name}};
push @return,$values[$i][$j];
}
return @return;} | sub get_entry
{ my ($self,$row,$column) = @_;
$row && $column || $self->throw("Need at least 2 ids");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
if(ref $matrix{$row}{$column}){
my ($i,$j) = @{$matrix{$row}{$column}};
return $values[$i][$j];
}
return;} | sub get_row
{ my ($self,$row) = @_;
$row || $self->throw("Need at least a row id");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @names = @{$self->names};
$matrix{$row} || return;
my @row = %{$matrix{$row}};
my $row_pointer = $row[1]->[0];
my $index = scalar(@names)-1;
return @{$values[$row_pointer]}[0..$index];} | sub names
{ my ($self,$val) = @_;
if($val){
$self->{"_names"} = $val;
}
return $self->{'_names'};} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($matrix,$values, $names,$file, $fh,$program) = $self->_rearrange([qw(MATRIX VALUES NAMES FILE FH PROGRAM)],@args);
($matrix && $values && $names) || $file || $fh || $self->throw("Need a file or file handle!");
$program && $self->program($program);
$self->_initialize_io(@args);
$self->_matrix($matrix) if $matrix;
$self->_values($values) if $values;
$self->names($names) if $names;
if(!$matrix && !$values && !$names){
$self->_parse();
}
return $self;} | sub print_matrix
{ my ($self) = @_;
my @names = @{$self->names};
my @values = @{$self->_values};
my %matrix = %{$self->_matrix};
my $str;
$str.= (" "x 4). scalar(@names)."\n";
foreach my $name (@names){
my $newname = $name. (" " x (15-length($name)));
$str.=$newname;
my $count = 0;
foreach my $n (@names){
my ($i,$j) = @{$matrix{$name}{$n}};
if($count < $#names){
$str.= $values[$i][$j]. " ";
}
else {
$str.= $values[$i][$j];
}
$count++;
}
$str.="\n";
}
return $str;} | sub program
{ my ($self,$val) = @_;
if($val){
$self->{'_program'} = $val;
}
return $self->{'_program'};} | General documentation
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".