NAME

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

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;

FEEDBACK

   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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

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

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

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

   new
        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

   run
        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)

   _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    : none