Raw content of Bio::Tools::Phylo::Molphy
<![CDATA[# $Id: Molphy.pm,v 1.3 2002/10/22 07:45:23 lapp Exp $
#
# BioPerl module for Bio::Tools::Phylo::Molphy
#
# Cared for by Jason Stajich <jason@bioperl.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::Tools::Phylo::Molphy - DESCRIPTION of Object
=head1 SYNOPSIS
use Bio::Tools::Phylo::Molphy;
my $parser = new Bio::Tools::Phylo::Molphy(-file => 'output.protml');
while( my $result = $parser->next_result ) {
}
=head1 DESCRIPTION
A parser for Molphy output (protml,dnaml)
=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/MailList.shtml - About the mailing lists
=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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::Tools::Phylo::Molphy;
use vars qw(@ISA);
use strict;
use Bio::Tools::Phylo::Molphy::Result;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::TreeIO;
use IO::String;
@ISA = qw(Bio::Root::Root Bio::Root::IO );
=head2 new
Title : new
Usage : my $obj = new Bio::Tools::Phylo::Molphy();
Function: Builds a new Bio::Tools::Phylo::Molphy object
Returns : Bio::Tools::Phylo::Molphy
Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : my $r = $molphy->next_result
Function: Get the next result set from parser data
Returns : Bio::Tools::Phylo::Molphy::Result object
Args : none
=cut
sub next_result{
my ($self) = @_;
# A little statemachine for the parser here
my ($state,$transition_ct,
@transition_matrix, %transition_mat, @resloc,) = ( 0,0);
my ( %subst_matrix, @treelines, @treedata, %frequencies);
my ( $treenum,$possible_trees, $model);
while( defined ( $_ = $self->_readline()) ) {
if( /^Relative Substitution Rate Matrix/ ) {
if( %subst_matrix ) {
$self->_pushback($_);
last;
}
$state = 0;
my ( @tempdata);
@resloc = ();
while( defined ($_ = $self->_readline) ) {
last if (/^\s+$/);
# remove leading/trailing spaces
s/^\s+//;
s/\s+$//;
my @data = split;
my $i = 0;
for my $l ( @data ) {
if( $l =~ /\D+/ ) {
push @resloc, $l;
}
$i++;
}
push @tempdata, \@data;
}
my $i = 0;
for my $row ( @tempdata ) {
my $j = 0;
for my $col ( @$row ) {
if( $i == $j ) {
# empty string for diagonals
$subst_matrix{$resloc[$i]}->{$resloc[$j]} = '';
} else {
$subst_matrix{$resloc[$i]}->{$resloc[$j]} = $col;
}
$j++;
}
$i++;
}
} elsif( /^Transition Probability Matrix/ ) {
if( /1\.0e7/ ) {
$state = 1;
$transition_ct = 0;
} else {
$state = 0;
}
} elsif ( /Acid Frequencies/ ) {
$state = 0;
$self->_readline(); # skip the next line
while( defined( $_ = $self->_readline) ) {
unless( /^\s+/) {
$self->_pushback($_);
last;
}
s/^\s+//;
s/\s+$//;
my ($index,$res,$model,$data) = split;
$frequencies{$res} = [ $model,$data];
}
} elsif( /^(\d+)\s*\/\s*(\d+)\s+(.+)\s+model/ ) {
my @save = ($1,$2,$3);
# finish processing the transition_matrix
my $i =0;
foreach my $row ( @transition_matrix ) {
my $j = 0;
foreach my $col ( @$row ) {
$transition_mat{$resloc[$i]}->{$resloc[$j]} = $col;
$j++;
}
$i++;
}
if( defined $treenum ) {
$self->_pushback($_);
last;
}
$state = 2;
($treenum,$possible_trees, $model) = @save;
$model =~ s/\s+/ /g;
} elsif( $state == 1 ) {
next if( /^\s+$/ );
s/^\s+//;
s/\s+$//;
# because the matrix is split up into 2-10 column sets
push @{$transition_matrix[$transition_ct++]}, split ;
$transition_ct = 0 if $transition_ct % 20 == 0;
} elsif( $state == 2 ) {
if( s/^(\d+)\s+(\-?\d+(\.\d+)?)\s+// ) {
push @treedata, [ $1,$2];
}
# save this for the end so that we can
# be efficient and only open one tree parser
push @treelines, $_;
}
}
# waiting till the end to do this, is it better
my @trees;
if( @treelines ) {
my $strdat = IO::String->new(join('',@treelines));
my $treeio = new Bio::TreeIO(-fh => $strdat,
-format => 'newick');
while( my $tree = $treeio->next_tree ) {
if( @treedata ) {
my $dat = shift @treedata;
# set the associated information
$tree->id($dat->[0]);
$tree->score($dat->[1]);
}
push @trees, $tree;
}
}
my $result = new Bio::Tools::Phylo::Molphy::Result
(-trees => \@trees,
-substitution_matrix => \%subst_matrix,
-transition_matrix => \%transition_mat,
-frequencies => \%frequencies,
-model => $model,
-search_space => $possible_trees,
);
}
1;
]]>