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Summary

Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy

Package variables

Included modules

Inherit

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

Synopsis

  use Bio::Tools::Run::Phylo::Semphy;

  # Make a Semphy factory
  $factory = Bio::Tools::Run::Phylo::Semphy->new();

  # Run Semphy with an alignment
  my $tree = $factory->run($alignfilename);

  # or with alignment object
  $tree = $factory->run($bio_simplalign);

  # you can supply an initial tree as well, which can be a newick tree file,
  # Bio::Tree::Tree object...
  $tree = $factory->run($bio_simplalign, $tree_obj);

  # ... or Bio::DB::Taxonomy object
  $tree = $factory->run($bio_simplalign, $bio_db_taxonomy);

  # (mixtures of all the above are possible)

  # $tree isa Bio::Tree::Tree

Description

This is a wrapper for running the Semphy application by N. Friedman et a.. You
can get details here: http://compbio.cs.huji.ac.il/semphy/. Semphy is used for
phylogenetic reconstruction (making a tree with branch lengths from an aligned
set of input sequences).
You can try supplying normal Semphy command-line arguments to new(), eg.
new(-hky => 1) or calling arg-named methods (excluding the initial hyphen(s),
eg. $factory->hky(1) to set the --hky switch to true).
Note that Semphy args are case-sensitive. To distinguish between Bioperl's
-verbose and the Semphy's --verbose, you must set Semphy's verbosity with
-semphy_verbose or the semphy_verbose() method.
You will need to enable this Semphy wrapper to find the Semphy program.
This can be done in (at least) three ways:

 1. Make sure the Semphy executable is in your path.
 2. Define an environmental variable SEMPHYDIR which is a 
    directory which contains the Semphy application:
    In bash:

    export SEMPHYDIR=/home/username/semphy/

    In csh/tcsh:

    setenv SEMPHYDIR /home/username/semphy

 3. Include a definition of an environmental variable SEMPHYDIR in
    every script that will use this Semphy wrapper module, e.g.:

    BEGIN { $ENV{SEMPHYDIR} = '/home/username/semphy/' }
    use Bio::Tools::Run::Phylo::Semphy;

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::Semphy->new()
 Function: creates a new Semphy factory
 Returns : Bio::Tools::Run::Phylo::Semphy
 Args    : Most options understood by Semphy can be supplied as key =>
           value pairs, with a true value for switches.

           These options can NOT be used with this wrapper (they are handled
           internally or don't make sense in this context):
           -h | --help | --fill-help
           -s | --sequence
           -t | --tree

           To distinguish between Bioperl's -verbose and the Semphy's --verbose,
           you must set Semphy's verbosity with -semphy_verbose

 Title   : run
 Usage   : $result = $factory->run($fasta_align_file);
           -or-
           $result = $factory->run($align_object);
           -or-
           $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 Semphy on an alignment.
 Returns : Bio::Tree::Tree
 Args    : The first argument represents an alignment, the second (optional)
           argument a species tree (to set an initial tree: normally the -t
           option to Semphy).
           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 where an initial tree was supplied, the alignment
           sequence names must correspond to node ids in the species tree.

 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),
                                               quiet => 'quiet'},
                                  -create => 1,
                                  -case_sensitive => 1);
    
    return $self;

}

sub run {

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

}

sub _run {

    my $self = shift;
    
    my $exe = $self->executable || return;
    
    my $aln_file = $self->_write_alignment;
    
    # generate a semphy-friendly tree file
    my $tree = $self->_tree;
    my $tree_file = '';
    if ($tree) {
        $tree = $self->_write_tree;
    }
    
    unless ($self->T) {
        my ($tfh, $tempfile) = $self->io->tempfile(-dir => $self->tempdir);
        $self->T($tempfile);
        close($tfh);
    }
    
    my $command = $exe.$self->_setparams($aln_file, $tree_file);
    $self->debug("semphy command = $command\n");
    
    open(my $pipe, "$command |") || $self->throw("semphy call ($command) failed to start: $? | $!");
    my $error = '';
    while (<$pipe>) {
        print unless $self->quiet;
        $error .= $_;
    }
    close($pipe) || ($error ? $self->warn("semphy call ($command) failed: $error") : $self->throw("semphy call ($command) crashed: $?"));
    
    my $result_file = $self->T();
    my $tio = Bio::TreeIO->new(-format => 'newick', -file => $result_file);
    my $result_tree = $tio->next_tree;
    
    return $result_tree;

}

sub _setparams {

    my ($self, $aln_file, $tree_file) = @_;
    
    my $param_string = ' -s '.$aln_file;
    $param_string .= ' -t '.$tree_file if $tree_file;
    
    my %methods = map { $_ => $_ } keys %PARAMS;
    $methods{'semphy_verbose'} = 'verbose';
    $param_string .= $self->SUPER::_setparams(-params =>\% methods,
                                              -switches => [keys %SWITCHES],
                                              -double_dash => 1);
    
    $param_string .= ' 2>&1';
    $param_string .= ' 1>/dev/null' if $self->quiet;
    
    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 _