Bio::Tools::Phylo::Gerp(3pm) User Contributed Perl Documentation Bio::Tools::Phylo::Gerp(3pm)NAME
Bio::Tools::Phylo::Gerp - Parses output from GERP
SYNOPSIS
use strict;
use Bio::Tools::Phylo::Gerp;
my $parser = Bio::Tools::Phylo::Gerp->new(-file => "alignment.rates.elems");
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 module is used to parse the output from 'GERP' (v2) by Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here:
http://mendel.stanford.edu/sidowlab/
It works on the .elems files produced by gerpelem.
Each result is a Bio::SeqFeature::Annotated representing a single constrained element.
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:
https://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 _
new
Title : new
Usage : my $obj = Bio::Tools::Phylo::Gerp->new();
Function: Builds a new Bio::Tools::Phylo::Gerp object
Returns : Bio::Tools::Phylo::Gerp
Args : -file (or -fh) should contain the contents of a gerpelem .elems file
next_result
Title : next_result
Usage : $result = $obj->next_result();
Function: Returns the next result available from the input, or undef if there
are no more results.
Returns : Bio::SeqFeature::Annotated object. Features are annotated with a tag
for 'pvalue', and a 'predicted' tag. They have no sequence id unless
the input GERP file is non-standard, with the seq id as the 6th
column.
NB: feature coordinates are alignment columns of the alignment
used to create the result file.
Args : none
perl v5.14.2 2012-03-02 Bio::Tools::Phylo::Gerp(3pm)
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Bio::Tools::Run::Phylo::Gerp(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Gerp(3pm)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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Gerp(3pm)