Provided by: libbio-perl-run-perl_1.7.1-3_all bug


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


         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;


       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: 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;


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AUTHOR - Sendu Bala



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

        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);
                  $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
                  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