| Bio::Tools::Run::Phylo::Gerp(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Gerp(3pm) |
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: 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;
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
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.
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/
Email bix@sendu.me.uk
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);
-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
| 2023-01-22 | perl v5.36.0 |