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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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 [email protected]

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