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#
# BioPerl module for Bio::Matrix::IO::mlagan
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
=head1 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;
=head1 DESCRIPTION
Use to read in and write out substitution matrix files suitable for use by
mlagan.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Matrix::IO::mlagan;
$Bio::Matrix::IO::mlagan::VERSION = '1.7.8';
use strict;
use Bio::Matrix::Mlagan;
use base qw(Bio::Matrix::IO);
=head2 new
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 :
=cut
=head2 next_matrix
Title : next_matrix
Usage : my $matrix = $obj->next_matrix();
Function: parses a matrix file
Returns : L<Bio::Matrix::Mlagan>
Args : none
=cut
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;
}
=head2 write_matrix
Title : write_matrix
Usage : $obj->write_matrix($matrix)
Function: Write out a matrix in mlagan format
Returns : n/a
Args : L<Bio::Matrix::Generic>
=cut
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;
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