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#
# BioPerl module for Bio::Matrix::IO::scoring
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies
=head1 SYNOPSIS
use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'scoring',
-file => 'BLOSUM50');
my $matrix = $parser->next_matrix;
=head1 DESCRIPTION
Describe the object here
=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 - Jason Stajich
Email jason-at-bioperl-dot-org
=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::scoring;
$Bio::Matrix::IO::scoring::VERSION = '1.7.8';
use strict;
use Bio::Matrix::Scoring;
use base qw(Bio::Matrix::IO);
=head2 new
Title : new
Usage : my $obj = Bio::Matrix::IO::scoring->new();
Function: Builds a new Bio::Matrix::IO::scoring object
Returns : an instance of Bio::Matrix::IO::scoring
Args :
=cut
=head2 next_matrix
Title : next_matrix
Usage : my $matrux = $parser->next_matrix
Function: parses a scoring matrix (BLOSUM,PAM styles)
Returns : L<Bio::Matrix::Scoring>
Args : none
=cut
sub next_matrix{
my ($self) = @_;
local ($_);
my (@matrix,@cols,@rows,%extras,$inmatrix);
while( defined ( $_ = $self->_readline ) ) {
next if ( /^\s*$/);
if( /^\#/ ) {
if( $inmatrix ) {
$self->_pushback($_);
last;
}
if( m/Entropy\s+\=\s+(\S+)\,\s+
Expected\s+\=\s+(\S+)/ox ) {
$extras{'-entropy'} = $1;
$extras{'-expected'} = $2;
} elsif ( m/Expected\s+score\s+\=\s+(\S+)\,
\s+Entropy\s+\=\s+(\S+)/xo ){
$extras{'-entropy'} = $2;
$extras{'-expected'} = $1;
} elsif( m/(PAM\s+\d+)\s+substitution.+
scale\s+\=\s+(\S+)\s+\=\s+(\S+)/ox ) {
$extras{'-matrix_name'} = $1;
$extras{'-scale'} = $2;
$extras{'-scale_value'} = $3;
} elsif( /Blocks Database\s+\=\s+(\S+)/o ) {
$extras{'-database'} = $1;
} elsif( m/(\S+)\s+Bit\s+Units/ox ) {
$extras{'-scale'} = $1;
} elsif( m/Lowest score\s+\=\s+(\S+)\,\s+
Highest score\s+\=\s+(\S+)/ox ) {
$extras{'-lowest_score'} = $1;
$extras{'-highest_score'} = $2;
} elsif( m/(Lambda)\s+\=\s+(\S+)\s+bits\,
\s+(H)\s+\=\s+(\S+)/ox ) {
# This is a DNA matrix
$extras{$1} = $2;
$extras{$3} = $4;
}
} elsif( s/^\s+(\S+)/$1/ ) {
@cols = split;
if( $cols[0] ne 'A' ) {
$self->warn("Unrecognized first line of matrix, we might not have parsed it correctly");
}
$inmatrix = 1;
} elsif( $inmatrix ) {
if( ! /^(\S+)/ ) { $inmatrix = 0; next }
my ($rowname,@row) = split;
push @rows, $rowname;
push @matrix, [@row];
} else {
print;
}
}
my $matrix = Bio::Matrix::Scoring->new(-values => \@matrix,
-rownames => \@rows,
-colnames => \@cols,
%extras);
}
=head2 write_matrix
Title : write_matrix
Usage : $matio->write_matrix($matrix)
Function: Write out a matrix in the BLOSUM/PAM format
Returns : none
Args : L<Bio::Matrix::Scoring>
=cut
sub write_matrix{
my ($self,@args) = @_;
$self->warn("cannot actually use this function yet - it isn't finished");
return;
}
1;
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