Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
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;
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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
Title : new Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out", -program=>"protdist"); Function: Constructor for PhylipDist Object Returns : L<Bio::Matrix::PhylipDist>
Title : _parse Usage : $matrix->_parse(); Function: internal method that parses the distance matrix file. Returns : Arguments:
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 : 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 : print_matrix Usage : $matrix->print_matrix(); Function: returns a string of the matrix in phylip format Returns : a string Arguments:
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 : names Usage : $matrix->names(); Function: get/set for array ref of names of sequences Returns : an array reference Arguments: an array reference
Title : program Usage : $matrix->program(); Function: get/set for the program name generating this matrix Returns : string Arguments: string
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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.