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Summary

Bio::Tools::Run::Gerp - Wrapper for GERP

Package variables

Included modules

Inherit

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

Synopsis

  use Bio::Tools::Run::Phylo::Gerp;

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

  # Run Gerp with an alignment and tree file
  my $parser = $factory->run($alignfilename, $treefilename);

  # or with alignment object and tree object (which needs branch lengths)
  $parser = $factory->run($bio_simplalign, $bio_tree_tree);

  # (mixtures of the above are possible)

  # look at the results
  while (my $feat = $parser->next_result) {
    my $start = $feat->start;
    my $end = $feat->end;
    my $rs_score = $feat->score;
    my $p_value = ($feat->annotation->get_Annotations('p-value'))[0]->value;
  }

Description

This is a wrapper for running the GERP (v2) programs 'gerpcol' and 'gerpelem' by
Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here:
http://mendel.stanford.edu/sidowlab/. GERP can be used for phylogenetic
footprinting/ shadowing (it finds 'constrained elements in multiple
alignments').
You can try supplying normal gerpcol/gerpelem command-line arguments to new(),
eg. $factory->new(-e => 0.05) or calling arg-named methods, eg.
$factory->e(0.05). The filename-related args (t, f, x) are handled internally
by the run() method. This wrapper currently only supports running GERP on a
single alignment at a time (ie. F isn't used at all, nor are multiple fs
possible).
You will need to enable this GERP wrapper to find the GERP executables.
This can be done in (at least) three ways:

 1. Make sure gerpcol and gerpelem are in your path.
 2. Define an environmental variable GERPDIR which is a 
    directory which contains the GERP executables:
    In bash:

    export GERPDIR=/home/username/gerp/

    In csh/tcsh:

    setenv GERPDIR /home/username/gerp

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

    BEGIN { $ENV{GERPDIR} = '/home/username/gerp/' }
    use Bio::Tools::Run::Phylo::Gerp;

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::Gerp->new()
 Function: creates a new GERP factory
 Returns : Bio::Tools::Run::Phylo::Gerp
 Args    : Most options understood by GERP can be supplied as key =>
           value pairs.

           These options can NOT be used with this wrapper:
           h, t, f, F and x

 Title   : run
 Usage   : $parser = $factory->run($align_file, $tree_file);
           -or-
           $parser = $factory->run($align_object, $tree_object);
 Function: Runs GERP on an alignment.
 Returns : Bio::Tools::Phylo::Gerp parser object, containing the results
 Args    : The first argument represents an alignment, the second argument
           a phylogenetic tree with branch lengths.
           The alignment can be provided as a MAF 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.

           In all cases, the alignment sequence names must correspond to node
           ids in the tree. Multi-word species names should have the
           spaces replaced with underscores (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    : none

Methods code

BEGIN {

    # lets add all the gerp executables to the path
    $PROGRAM_DIR = $ENV{'GERPDIR'};
    $ENV{PATH} = "$PROGRAM_DIR:$ENV{PATH}" if $PROGRAM_DIR;

}

sub program_name {

    my $self = shift;
    if (@_) { $self->{program_name} = shift }
    return $self->{program_name} || $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 => [@COLPARAMS, @ELEMPARAMS,
                                               @SWITCHES, 'quiet'],
                                  -create => 1);
    
    return $self;

}

sub run {

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

}

sub _run {

    my $self = shift;
    
    $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'");
    
    foreach my $prog ('gerpcol', 'gerpelem') {
        delete $self->{'_pathtoexe'};
        $self->program_name($prog);
        my $exe = $self->executable || $self->throw("'$prog' executable not found");
        
        my $command = $exe.$self->_setparams($prog);
        $self->debug("gerp command = $command\n");
        
        #eval {
        #    local $SIG{ALRM} = sub { die "alarm\n" };
        #    alarm 60;
        #    system($command) && $self->throw("gerp call ($command) failed: $! | $?");
        #    alarm 0;
        #};
        #die if $@ && $@ ne "alarm\n";
        #if ($@) {
        #    die "Gerp timed out\n";
        #}
        #
        # system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
        
        open(my $pipe, "$command |") || $self->throw("gerp call ($command) failed to start: $? | $!");
        my $error = '';
        my $warning = '';
        while (<$pipe>) {
            if ($self->quiet) {
                $error .= $_;
                $warning .= $_ if /warning/i;
            }
            else {
                print;
            }
        }
        close($pipe) || ($error ? $self->throw("gerp call ($command) failed: $error") : $self->throw("gerp call ($command) crashed: $?"));
        
        # (throws most likely due to seg fault in gerpelem when ~25000 entries
        #  in rates file, not much I can do about it!)
        
        $self->warn("GERP: ".$warning) if $warning;
    }
    
    #system("rm -fr $cwd/gerp_dir; cp -R $temp_dir $cwd/gerp_dir");
    
    my $result_file = $self->{align_base}.'.rates.elems';
    my $parser = Bio::Tools::Phylo::Gerp->new(-file => $result_file);
    
    # cd back again
    chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'");
    
    return $parser;

}

sub _setparams {

    my ($self, $prog) = @_;
    
    my $param_string;
    if ($prog eq 'gerpcol') {
        my $align_file = $self->_write_alignment;
        $param_string .= ' -f '.$align_file;
        $self->{align_base} = basename($align_file);
        $param_string .= ' -t '.$self->_write_tree;
        $param_string .= $self->SUPER::_setparams(-params =>\@ COLPARAMS,
                                                  -switches =>\@ SWITCHES,
                                                  -dash => 1);
    }
    else {
        $param_string .= ' -f '.$self->{align_base}.'.rates';
        $param_string .= $self->SUPER::_setparams(-params =>\@ ELEMPARAMS,
                                                  -switches =>\@ SWITCHES,
                                                  -dash => 1);
    }
    
    $param_string .= " 2>&1";
    
    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 _