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#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

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

=head1 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;
  }

=head1 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-E<gt>new(-e =E<gt> 0.05) or calling arg-named methods, eg.
$factory-E<gt>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;

=head1 FEEDBACK

=head2 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

=head2 Support 

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

I<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.

=head2 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/

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=head1 APPENDIX

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

=cut

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

use Cwd;
use File::Spec;
use File::Basename;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Phylo::Gerp;

use base qw(Bio::Tools::Run::Phylo::PhyloBase);