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.IX Title "Bio::Tools::Run::Phylo::Gerp 3pm"
.TH Bio::Tools::Run::Phylo::Gerp 3pm "2021-01-06" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Tools::Run::Gerp \- Wrapper for GERP
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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(\*(Aqp\-value\*(Aq))[0]\->value;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper for running the \s-1GERP\s0 (v2) programs 'gerpcol' and 'gerpelem' by
Eugene Davydov (originally Gregory M. Cooper et al.). You can get details here:
http://mendel.stanford.edu/sidowlab/. \s-1GERP\s0 can be used for phylogenetic
footprinting/ shadowing (it finds 'constrained elements in multiple
alignments').
.PP
You can try supplying normal gerpcol/gerpelem command-line arguments to \fBnew()\fR,
eg. \f(CW$factory\fR\->new(\-e => 0.05) or calling arg-named methods, eg.
\&\f(CW$factory\fR\->e(0.05). The filename-related args (t, f, x) are handled internally
by the \fBrun()\fR method. This wrapper currently only supports running \s-1GERP\s0 on a
single alignment at a time (ie. F isn't used at all, nor are multiple fs
possible).
.PP
You will need to enable this \s-1GERP\s0 wrapper to find the \s-1GERP\s0 executables.
This can be done in (at least) three ways:
.PP
.Vb 4
\& 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} = \*(Aq/home/username/gerp/\*(Aq }
\&    use Bio::Tools::Run::Phylo::Gerp;
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : None
.Ve
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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
.Ve
.SS "run"
.IX Subsection "run"
.Vb 10
\& 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)
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 5
\& 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
.Ve