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# $Id$
# BioPerl module for Bio::Tools::Run::Phylo::Phast::PhyloFit
# Please direct questions and support issues to <>
# Cared for by Sendu Bala <>
# Copyright Sendu Bala
# 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::Phast::PhyloFit - Wrapper for phyloFit
use Bio::Tools::Run::Phylo::Phast::PhyloFit;
# Make a PhyloFit factory
$factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new();
# Generate an init.mod file for use by phastCons
my $init_file = $factory->run($alignment, $tree);
This is a wrapper for running the phyloFit application by Adam Siepel. You
can get details here:
Currently the interface is extremely simplified. Only the --tree form of usage
is allowed (not --init-model), which means a tree must be supplied with the
alignment (to run()). You can try supplying normal phyloFit arguments to new(),
or calling arg-named methods (excluding initial hyphens and converting others
to underscores, eg. $factory-E<gt>gaps_as_bases(1) to set the --gaps-as-bases arg).
WARNING: the API may change in the future to allow for greater flexability and
access to more phyloFit features.
You will need to enable this PhyloFit wrapper to find the phast programs (at
least phyloFit itself).
This can be done in (at least) three ways:
1. Make sure the phyloFit executable is in your path.
2. Define an environmental variable PHASTDIR which is a
directory which contains the phyloFit application:
In bash:
export PHASTDIR=/home/username/phast/bin
In csh/tcsh:
setenv PHASTDIR /home/username/phast/bin
3. Include a definition of an environmental variable PHASTDIR in
every script that will use this PhyloFit wrapper module, e.g.:
BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
use Bio::Tools::Run::Phylo::Phast::PhyloFit;
=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. - General discussion - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
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:
=head1 AUTHOR - Sendu Bala
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
package Bio::Tools::Run::Phylo::Phast::PhyloFit;
use strict;
use Cwd;
use File::Spec;
use Bio::AlignIO;
use Bio::TreeIO;
use base qw(Bio::Tools::Run::Phylo::PhyloBase);
our $PROGRAM_NAME = 'phyloFit';
# methods and their synonyms from the phastCons args we support
our %PARAMS = (subst_mod => 's',
min_informative => 'I',
precision => 'p',
log => 'l',
ancestor => 'A',
nrates => 'k',
alpha => 'a',
rate_constants => 'K',
features => 'g',
catmap => 'c',
do_cats => 'C',
reverse_groups => 'R');
our %SWITCHES = (gaps_as_bases => 'G',
quiet => 'q',
EM => 'E',
init_random => 'r',
estimate_freqs => 'F',
markov => 'N',
non_overlapping => 'V');
# just to be explicit, args we don't support (yet) or we handle ourselves
our %UNSUPPORTED = (msa_format => 'i',
out_root => 'o',
tree => 't',
help => 'h',
lnl => 'L',
init_model => 'M',
scale_only => 'B',
scale_subtree => 'S',
no_freqs => 'f',
no_rates => 'n',
post_probs => 'P',
expected_subs => 'X',
expected_total_subs => 'Z',
column_probs => 'U',
windows => 'w',
windows_explicit => 'v');
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : None
sub program_name {
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : None
sub program_dir {
return $PROGRAM_DIR;
=head2 new
Title : new
Usage : $factory = Bio::Tools::Run::Phylo::Phast::PhyloFit->new()
Function: creates a new PhyloFit factory
Returns : Bio::Tools::Run::Phylo::Phast::PhyloFit
Args : Most options understood by phastCons can be supplied as key =>
value pairs. Options that don't normally take a value
should be given a value of 1. You can type the keys as you would on
the command line (eg. '--gaps-as-bases' => 1) or with only a single
hyphen to start and internal hyphens converted to underscores (eg.
-gaps_as_bases => 1) to avoid having to quote the key.
These options can NOT be used with this wrapper currently:
msa_format / i
out_root / o
tree / t
help / h
lnl / L
init_model / M
scale_only / B
scale_subtree / S
no_freqs / f
no_rates / n
post_probs / P
expected_subs / X
expected_total_subs / Z
column_probs / U
windows / w
windows_explicit / v
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_set_from_args(\@args, -methods => {(map { $_ => $PARAMS{$_} } keys %PARAMS),
(map { $_ => $SWITCHES{$_} } keys %SWITCHES)},
-create => 1);
return $self;
=head2 run
Title : run
Usage : $result = $factory->run($fasta_align_file, $newick_tree_file);
$result = $factory->run($align_object, $tree_object);
$result = $factory->run($align_object, $db_taxonomy_object);
Function: Runs phyloFit on an alignment.
Returns : filename of init.mod file produced
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
filename, or a Bio::Align::AlignI compliant object (eg. a
The species tree can be provided as a newick format tree filename
or a Bio::Tree::TreeI compliant object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
In all cases, the alignment sequence names must correspond to node
ids in the species tree. Multi-word species names should be joined
with underscores to form the sequence names, eg. Homo_sapiens
sub run {
my ($self, $aln, $tree) = @_;
($aln && $tree) || $self->throw("alignment and tree must be supplied");
$tree = $self->_tree($tree);
# adjust tree node ids to convert spaces to underscores (eg. if tree
# generated from taxonomy)
foreach my $node ($tree->get_leaf_nodes) {
my $id = $node->id;
$id =~ s/ /_/g;
# check node and seq names match
return $self->_run;
sub _run {
my $self = shift;
my $exe = $self->executable || return;
# cd to a temp dir
my $temp_dir = $self->tempdir;
my $cwd = Cwd->cwd();
chdir($temp_dir) || $self->throw("Couldn't change to temp dir '$temp_dir'");
my $aln_file = $self->_write_alignment;
my $tree_file = $self->_write_tree;
#...phyloFit --tree "(human,(mouse,rat))" --msa-format FASTA --out-root init alignment.fa
my $command = $exe.$self->_setparams($aln_file, $tree_file);
$self->debug("phyloFit command = $command\n");
system($command) && $self->throw("phyloFit call ($command) crashed: $?");
# cd back again
chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'");
return File::Spec->catfile($temp_dir, 'init.mod');
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Creates a string of params to be used in the command string
Returns : string of params
Args : alignment and tree file names
sub _setparams {
my ($self, $aln_file, $tree_file) = @_;
my $param_string = ' --tree '.$tree_file;
$param_string .= ' --msa-format FASTA';
$param_string .= ' --out-root init';
# --min-informative defaults to 50, but must not be greater than the number
# of bases in the alignment
my $aln = $self->_alignment;
my $length = $aln->length;
my $min_informative = $self->min_informative || 50;
if ($length < $min_informative) {
$param_string .= $self->SUPER::_setparams(-params => [keys %PARAMS],
-switches => [keys %SWITCHES],
-double_dash => 1,
-underscore_to_dash => 1);
$param_string .= ' '.$aln_file;
return $param_string;