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# BioPerl module for Bio::Tools::Run::Phylo::Phylip::ProtDist
#
# Created by
#
# Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip
program protdist
=head1 SYNOPSIS
#Create a SimpleAlign object
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
$inputfilename = 't/data/cysprot.fa';
$aln = $factory->run($inputfilename); # $aln is a SimpleAlign object.
# Create the Distance Matrix using a default PAM matrix and id name
# lengths limit of 30 note to use id name length greater than the
# standard 10 in protdist, you will need to modify the protdist source
# code
@params = ('MODEL' => 'PAM');
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my ($matrix) = $protdist_factory->run($aln); # an array of Bio::Matrix::PhylipDist matrix
#finding the distance between two sequences
my $distance = $matrix->get_entry('protein_name_1','protein_name_2');
my @column = $matrix->get_column('protein_name_1');
my @row = $martrix->get_row('protein_name_1');
my @diag = $matrix->get_diagonal();
print $matrix->print_matrix;
#Alternatively, one can create the matrix by passing in a file
#name containing a multiple alignment in phylip format
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my ($matrix) = $protdist_factory->run('/home/shawnh/prot.phy');
=head1 DESCRIPTION
Wrapper for protdist Joseph Felsentein for creating a distance matrix
comparing protein sequences from a multiple alignment file or a
L<Bio::SimpleAlign> object and returns a L<Bio::Matrix::PhylipDist> object;
VERSION Support
This wrapper currently supports v3.5 of phylip. There is also support
for v3.6.
=head1 PARAMETERS FOR PROTDIST COMPUTATION
=head2 MODEL
Title : MODEL
Description : (optional)
This sets the model of amino acid substitution used
in the calculation of the distances. 3 different
models are supported:
PAM Dayhoff PAM Matrix(default)
KIMURA Kimura's Distance CAT
Categories Distance Usage: @params =
('model'=>'X');#where X is one of the values above
Defaults to PAM For more information on the usage of
the different models, please refer to the
documentation
defaults to Equal
(0.25,0.25,0.25,0.25) found in the phylip package.
Additional models in PHYLIP 3.6
PMB - Henikoff/Tillier PMB matrix
JTT - Jones/Taylor/Thornton
=head2 MULTIPLE
Title : MULTIPLE
Description: (optional)
This allows multiple distance matrices to be generated from multiple
MSA.
Usage: @params = ('MULTIPLE'=>100) where the value specifyies the
number of aligments given.
=head2 ALL SUBSEQUENT PARAMETERS WILL ONLY WORK IN CONJUNCTION WITH
THE Categories Distance MODEL*
=head2 GENCODE
Title : GENCODE
Description : (optional)
This option allows the user to select among various
nuclear and mitochondrial genetic codes.
Acceptable Values:
U Universal
M Mitochondrial
V Vertebrate mitochondrial
F Fly mitochondrial
Y Yeast mitochondrial
Usage : @params = ('gencode'=>'X');
where X is one of the letters above
Defaults to U
=head2 CATEGORY
Title : CATEGORY
Description : (optional)
This option sets the categorization of amino acids
all have groups: (Glu Gln Asp Asn), (Lys Arg His),
(Phe Tyr Trp) plus:
G George/Hunt/Barker:
(Cys), (Met Val Leu Ileu),
(Gly Ala Ser Thr Pro)
C Chemical:
(Cys Met), (Val Leu Ileu Gly Ala Ser Thr),
(Pro)
H Hall:
(Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr),
(Pro)
Usage : @params = ('category'=>'X');
where X is one of the letters above
Defaults to G
=head2 PROBCHANGE
Title : PROBCHANGE
Description : (optional)
This option sets the ease of changing category of amino
acid. (1.0 if no difficulty of changing,less if less
easy. Can't be negative)
Usage : @params = ('probchange'=>X) where 0<=X<=1
Defaults to 0.4570
=head2 TRANS
Title : TRANS
Description : (optional)
This option sets transition/transversion ratio can be
any positive number
Usage : @params = ('trans'=>X) where X >= 0
Defaults to 2
=head2 FREQ
Title : FREQ
Description : (optional)
This option sets the frequency of each base (A,C,G,T)
The sum of the frequency must sum to 1.
For example A,C,G,T = (0.25,0.5,0.125,0.125)
Usage : @params = ('freq'=>('W','X','Y','Z')
where W + X + Y + Z = 1
Defaults to Equal (0.25,0.25,0.25,0.25)
=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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@PROTDIST_PARAMS @OTHER_SWITCHES
%OK_FIELD);
use strict;
use Cwd;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);
# You will need to enable the protdist program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable CLUSTALDIR in
# every script that will use Clustal.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';
#
# 3. You can set the path to the program through doing:
# my @params('program'=>'/usr/local/bin/protdist');
# my $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
#
BEGIN {
@PROTDIST_PARAMS = qw(MODEL GENCODE CATEGORY PROBCHANGE TRANS WEIGHTS FREQ MULTIPLE);
@OTHER_SWITCHES = qw(QUIET);
foreach my $attr(@PROTDIST_PARAMS,@OTHER_SWITCHES) {
$OK_FIELD{$attr}++;
}
}
=head2 program_name
Title : program_name
Usage : >program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'protdist';
}
=head2 program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtiained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) {
$self->executable($value);
next;
}
if ($attr =~ /IDLENGTH/i){
$self->idlength($value);
next;
}
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 idlength
Title : idlength
Usage : $obj->idlength ($newval)
Function:
Returns : value of idlength
Args : newvalue (optional)
=cut
sub idlength{
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'idlength'} = $value;
}
return $self->{'idlength'};
}
=head2 run
Title : run
Usage :
$inputfilename = 't/data/prot.phy';
$matrix= $prodistfactory->run($inputfilename);
or
$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $protdistfactory->align($seq_array_ref);
$matrix = $protdistfactory->run($aln);
Function: Create a distance matrix from a SimpleAlign object or a multiple alignment file
Example :
Returns : L<Bio::Matrix::PhylipDist>
Args : Name of a file containing a multiple alignment in Phylip format
or an SimpleAlign object
Throws an exception if argument is not either a string (eg a
filename) or a Bio::SimpleAlign object. If
argument is string, throws exception if file corresponding to string
name can not be found.
=cut
sub run{
my ($self,$input) = @_;
my ($infilename);
# Create input file pointer
$infilename = $self->_setinput($input);
if (!$infilename) {$self->throw("Problems setting up for protdist. Probably bad input data in $input !");}
# Create parameter string to pass to protdist program
my $param_string = $self->_setparams();
# run protdist
my @mat = $self->_run($infilename,$param_string);
return wantarray ? @mat:\@mat;
}
#################################################
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to protdist program
Example :
Returns : Bio::Tree object
Args : Name of a file containing a set of multiple alignments in Phylip format
and a parameter string to be passed to protdist
=cut
sub _run {
my ($self,$infile,$param_string) = @_;
my $instring;
my $curpath = cwd;
unless( File::Spec->file_name_is_absolute($infile) ) {
$infile = $self->io->catfile($curpath,$infile);
}
$instring = $infile."\n$param_string";
$self->debug( "Program ".$self->executable." $instring\n");
chdir($self->tempdir);
#open a pipe to run protdist to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) {
open(PROTDIST,"|".$self->executable .">/dev/null");
}
else {
open(PROTDIST,"|".$self->executable);
}
print PROTDIST $instring;
close(PROTDIST);
# get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile);
chdir($curpath);
$self->throw("protdist did not create matrix correctly ($outfile)")
unless (-e $outfile);
#Create the distance matrix here
my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file=>$outfile);
my @matrix;
while (my $mat = $parser->next_matrix){
push @matrix, $mat;
}
# Clean up the temporary files created along the way...
unlink $outfile unless $self->save_tempfiles;
return @matrix;
}
=head2 create_distance_matrix
Title : create_distance_matrix
Usage : my $file = $app->create_distance_matrix($treefile);
Function: This method is deprecated. Please use run method.
Returns : L<Bio::Matrix::PhylipDist>
Args : Name of a file containing a multiple alignment in Phylip format
or an SimpleAlign object
Throws an exception if argument is not either a string (eg a
filename) or a Bio::SimpleAlign object. If
argument is string, throws exception if file corresponding to string
name can not be found.
=cut
sub create_distance_matrix{
return shift->run(@_);
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for protdist program
Example :
Returns : name of file containing a multiple alignment in Phylip format
Args : SimpleAlign object reference or input file name
=cut
sub _setinput {
my ($self, $input) = @_;
my ($alnfilename,$tfh);
# suffix is used to distinguish alignment files from an align obkect
#If $input is not a reference it better be the name of a file with the sequence/
# a phy formatted alignment file
unless (ref $input) {
# check that file exists or throw
$alnfilename= $input;
unless (-e $input) {return 0;}
return $alnfilename;
}
my @input = ref $input eq 'ARRAY' ? @{$input} : ($input);
# $input may be a SimpleAlign Object
($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
my $alnIO = Bio::AlignIO->new(-fh => $tfh,
-format=>'phylip',
-idlength=>$self->idlength());
my $input_count = 0;
foreach my $input(@input){
if ($input->isa("Bio::SimpleAlign")){
# Open temporary file for both reading & writing of BioSeq array
$alnIO->write_aln($input);
}
$input_count++;
}
$alnIO->close();
close($tfh);
$tfh = undef;
$self->_input_nbr($input_count);
return $alnfilename;
}
sub _input_nbr {
my ($self,$val) = @_;
if($val){
$self->{'_input_nbr'} = $val;
}
return $self->{'_input_nbr'};
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for protdist program
Example :
Returns : parameter string to be passed to protdist
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
#do nothing for now
$self = shift;
my $param_string = "";
my $cat = 0;
my %menu = %{$Menu{$self->version}->{'PROTDIST'}};
foreach my $attr ( @PROTDIST_PARAMS) {
$value = $self->$attr();
next unless (defined $value);
if ($attr =~/MODEL/i){
if ($value=~/CAT/i){
$cat = 1;
}
$param_string .= $menu{'MODEL'}{$value};
}
if($attr=~/MULTIPLE/i){
$param_string.=$menu{'MULTIPLE'}."$value\n";
}
if ($cat == 1){
if($attr =~ /GENCODE/i){
my $allowed = $menu{'GENCODE'}{'ALLOWED'};
$self->throw("Unallowed value for genetic code") unless ($value =~ /[$allowed]/);
$param_string .= $menu{'GENCODE'}{'OPTION'}."$value\n";
}
if ($attr =~/CATEGORY/i){
my $allowed = $menu{'CATEGORY'}{'ALLOWED'};
$self->throw("Unallowed value for categorization of amino acids") unless ($value =~/[$allowed]/);
$param_string .= $menu{'CATEGORY'}{'OPTION'}."$value\n";
}
if ($attr =~/PROBCHANGE/i){
if (($value =~ /\d+/)&&($value >= 0) && ($value < 1)){
$param_string .= $menu{'PROBCHANGE'}."$value\n";
}
else {
$self->throw("Unallowed value for probability change category");
}
}
if ($attr =~/TRANS/i){
if (($value=~/\d+/) && ($value >=0)){
$param_string .=$menu{'TRANS'}."$value\n";
}
}
if ($attr =~ /FREQ/i){
my @freq = split(",",$value);
if ($freq[0] !~ /\d+/){ #a letter provided (sets frequencies equally to 0.25)
$param_string .=$menu{'FREQ'}.$freq[0]."\n";
}
elsif ($#freq == 3) {#must have 4 digits for each base
$param_string .=$menu{'FREQ'};
foreach my $f (@freq){
$param_string.="$f\n";
}
}
else {
$self->throw("Unallowed value for base frequencies");
}
}
}
}
#set multiple option is not set and there are more than one sequence
if (($param_string !~ $menu{'MULTIPLE'}) && (defined ($self->_input_nbr) &&($self->_input_nbr > 1))){
$param_string.=$menu{'MULTIPLE'}.$self->_input_nbr."\n";
}
$param_string .=$menu{'SUBMIT'};
return $param_string;
}
=head1 Bio::Tools::Run::Wrapper methods
=cut
=head2 no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
=cut
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
=cut
=head2 outfile_name
Title : outfile_name
Usage : my $outfile = $protdist->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
=cut
=head2 tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a ProtDist run
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
1; # Needed to keep compiler happy