Bio::Tools::Phylo Molphy
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Summary
Bio::Tools::Phylo::Molphy - parser for Molphy output
Package variables
No package variables defined.
Included modules
Bio::Tools::Phylo::Molphy::Result
Bio::TreeIO
IO::String
Inherit
Bio::Root::IO Bio::Root::Root
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 }
Description
A parser for Molphy output (protml,dnaml)
Methods
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $r = $molphy->next_result
Function: Get the next result set from parser data
Returns : Bio::Tools::Phylo::Molphy::Result object
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);

  return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
   my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _