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Summary

Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit

Package variables

Included modules

Inherit

Bio::Tools::Run::Phylo::PhyloBase

Synopsis

  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);

Description

This is a wrapper for running the phyloFit application by Adam Siepel. You
can get details here: http://compgen.bscb.cornell.edu/~acs/software.html
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->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;

Methods

Methods description

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

 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

 Title   : run
 Usage   : $result = $factory->run($fasta_align_file, $newick_tree_file);
           -or-
           $result = $factory->run($align_object, $tree_object);
           -or-
           $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
           Bio::SimpleAlign).
           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

 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

Methods code

sub program_name {

    return $PROGRAM_NAME;

}

sub program_dir {

    return $PROGRAM_DIR;

}

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;

}

sub run {

    my ($self, $aln, $tree) = @_;
    
    ($aln && $tree) || $self->throw("alignment and tree must be supplied");
    $self->_alignment($aln);
    $tree = $self->_tree($tree);
    
    $tree->force_binary;
    
    # 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;
        $node->id($id);
    }
    
    # check node and seq names match
    $self->_check_names;
    
    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');

}

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) {
        $self->min_informative($length);
    }
    
    $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;
}

1;

}

General documentation

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with code and data examples if at all possible.

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _