Bio::Matrix::IO
mlagan
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Summary
Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
-file => 'nucmatrix.txt');
my $matrix = $parser->next_matrix;
my $gap_open = $parser->gap_open;
my $gap_continue = $parser->gap_continue;
Description
Use to read in and write out substitution matrix files suitable for use by
mlagan.
Methods
Methods description
Title : next_matrix
Usage : my $matrix = $obj->next_matrix();
Function: parses a matrix file
Returns : Bio::Matrix::Mlagan
Args : none |
Title : write_matrix
Usage : $obj->write_matrix($matrix)
Function: Write out a matrix in mlagan format
Returns : n/a
Args : Bio::Matrix::Generic |
Methods code
sub next_matrix
{ my $self = shift;
my (@matrix, $gap_open, $gap_cont);
while (defined ($_ = $self->_readline)) {
if (/^[ACGTN\.]/) {
my (undef, @values) = split;
push(@matrix,\@ values);
}
elsif (/^[-\d]/) {
($gap_open, $gap_cont) = split;
last;
}
}
@matrix == 6 || $self->throw("Something wrong with file, was it the correct format?");
my $matrix = Bio::Matrix::Mlagan->new(-values =>\@ matrix,
-gap_open => $gap_open,
-gap_continue => $gap_cont);
return $matrix;} | sub write_matrix
{ my ($self, $matrix) = @_;
$matrix || $self->throw("Matrix required as input");
my $gap_open = $matrix->gap_open;
my $gap_continue = $matrix->gap_continue;
unless (defined $gap_open && defined $gap_continue) {
$self->throw("gap_open() and gap_continue() in the supplied matrix object must both be set");
}
$self->_print(" A C G T . N\n");
foreach my $char (qw(A C G T . N)) {
my @row = $matrix->get_row($char);
my $row = $char;
foreach my $val (@row) {
$row .= " " x (5 - length($val)) . $val;
}
$self->_print($row."\n");
}
$self->_print("\n$gap_open $gap_continue");
return;
}
1;} | General documentation
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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 $obj = Bio::Matrix::IO::mlagan->new();
Function: Builds a new Bio::Matrix::IO::mlagan object
Returns : an instance of Bio::Matrix::IO::mlagan
Args :