#
# BioPerl module for Bio::Tools::Phylo::Molphy
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-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 - parser for Molphy output
=head1 SYNOPSIS
use Bio::Tools::Phylo::Molphy;
my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml');
while( my $r = $parser->next_result ) {
# r is a Bio::Tools::Phylo::Molphy::Result object
# print the model name
print $r->model, "\n";
# get the substitution matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# substitution rate
my $smat = $r->substitution_matrix;
print "Arg -> Gln substitution rate is %d\n",
$smat->{'Arg'}->{'Gln'}, "\n";
# get the transition probablity matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# transition probabilty
my $tmat = $r->transition_probability_matrix;
print "Arg -> Gln transition probablity is %.2f\n",
$tmat->{'Arg'}->{'Gln'}, "\n";
# get the frequency for each of the residues
my $rfreqs = $r->residue_frequencies;
foreach my $residue ( keys %{$rfreqs} ) {
printf "residue %s expected freq: %.2f observed freq: %.2f\n",
$residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
}
my @trees;
while( my $t = $r->next_tree ) {
push @trees, $t;
}
print "search space is ", $r->search_space, "\n",
"1st tree score is ", $trees[0]->score, "\n";
# writing to STDOUT, use -file => '>filename' to specify a file
my $out = Bio::TreeIO->new(-format => "newick");
$out->write_tree($trees[0]); # writing only the 1st tree
}
=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/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.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::Tools::Phylo::Molphy;
use strict;
use Bio::Tools::Phylo::Molphy::Result;
use Bio::TreeIO;
use IO::String;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Phylo::Molphy->new();
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, $model);
my ($trans_type,$trans_amount);
my $parsed = 0;
while( defined ( $_ = $self->_readline()) ) {
$parsed = 1;
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\.0e(5|7))\)\s+(\S+)/ ) {
$state = 1;
my $newtrans_type = "$3-$1";
$trans_amount = $1;
if( defined $trans_type ) {
# finish processing the transition_matrix
my $i =0;
foreach my $row ( @transition_matrix ) {
my $j = 0;
foreach my $col ( @$row ) {
$transition_mat{$trans_type}->{$resloc[$i]}->{$resloc[$j]} = $col;
$j++;
}
$i++;
}
}
$trans_type = $newtrans_type;
$transition_ct = 0;
@transition_matrix = ();
}
} 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 ) {
$transition_mat{$trans_type}->{$resloc[$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+Ala/);
s/^\s+//;
s/\s+$//;
if( $trans_type eq '1PAM-1.0e7' ) {
# because the matrix is split up into 2-10 column sets
push @{$transition_matrix[$transition_ct++]}, split ;
$transition_ct = 0 if $transition_ct % 20 == 0;
} elsif( $trans_type eq '1PAM-1.0e5' ) {
# because the matrix is split up into 2-10 column sets
my ($res,@row) = split;
next if $transition_ct >= 20; # skip last
push @{$transition_matrix[$transition_ct++]}, @row;
}
} 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 = Bio::TreeIO->new(-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;
}
}
return unless( $parsed );
my $result = Bio::Tools::Phylo::Molphy::Result->new
(-trees => \@trees,
-substitution_matrix => \%subst_matrix,
-frequencies => \%frequencies,
-model => $model,
-search_space => $possible_trees,
);
while( my ($type,$mat) = each %transition_mat ) {
$result->transition_probability_matrix( $type,$mat);
}
$result;
}
1;