Bio::Tools::Run::Simprot(3pm) User Contributed Perl Documentation Bio::Tools::Run::Simprot(3pm)
NAME
Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a
phylogenetic tree
SYNOPSIS
use Bio::Tools::Run::Simprot;
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(
-format => 'nh', -file => 't/data/tree.nh');
my $tree = $treeio->next_tree;
my $simprot = Bio::Tools::Run::Simprot->new();
$simprot->tree($tree);
my ($rc,$aln,$seq) = $simprot->run();
DESCRIPTION
This is a wrapper around the Simprot program by Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier.
Simprot allows for several models of amino acid substitution (PAM, JTT and PMB), allows for gamma distributed sites rates according to
Yang's model, and implements a parameterised Qian and Goldstein distribution model for insertion and deletion.
See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more information.
Helping the module find your executable
You will need to enable SIMPROTDIR to find the simprot program. This can be done in (at least) three ways:
1. Make sure the simprot executable is in your path (i.e.
'which simprot' returns a valid program
2. define an environmental variable SIMPROTDIR which points to a
directory containing the 'simprot' app:
In bash
export SIMPROTDIR=/home/progs/simprot or
In csh/tcsh
setenv SIMPROTDIR /home/progs/simprot
3. include a definition of an environmental variable SIMPROTDIR
in every script that will
BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
use Bio::Tools::Run::Simprot;
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 one
of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Albert Vilella
Email avilella-at-gmail-dot-com
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 :
new
Title : new
Usage : my $simprot = Bio::Tools::Run::Simprot->new();
Function: Builds a new Bio::Tools::Run::Simprot
Returns : Bio::Tools::Run::Simprot
Args : -alignment => the Bio::Align::AlignI object
-tree => the Bio::Tree::TreeI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-executable => where the simprot executable resides
-params => A reference to a hash where keys are parameter names
and hash values are the associated parameter values
See also: Bio::Tree::TreeI, Bio::Align::AlignI
set_parameters
Title : set_parameters
Usage : $codeml->set_parameters($parameter, $value);
Function: (Re)set the SimProt parameters
Returns : none
Args : First argument is the parameter name
Second argument is the parameter value
set_default_parameters
Title : set_default_parameters
Usage : $codeml->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
get_parameters
Title : get_parameters
Usage : my %params = $self->get_parameters();
Function: returns the list of parameters as a hash
Returns : associative array keyed on parameter names
Args : none
prepare
Title : prepare
Usage : my $rundir = $simprot->prepare();
Function: prepare the simprot analysis using the default or updated parameters
the alignment parameter and species tree must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
run
Title : run
Usage : my $nhx_tree = $simprot->run();
Function: run the simprot analysis using the default or updated parameters
the alignment parameter must have been set
Returns : L<Bio::Tree::TreeI> object [optional]
Args : L<Bio::Align::AlignI> object
L<Bio::Tree::TreeI> object
error_string
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
alignment
Title : alignment
Usage : $simprot->align($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Args : [optional] L<Bio::Align::AlignI>
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::SimpleAlign>
tree
Title : tree
Usage : $simprot->tree($tree, %params);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
[optional] %parameters => hash of tree-specific parameters
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::Tree::Tree>
Bio::Tools::Run::BaseWrapper methods
save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_name
Title : outfile_name
Usage : my $outfile = $simprot->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanup
Title : cleanup
Usage : $simprot->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
perl v5.12.3 2011-06-18 Bio::Tools::Run::Simprot(3pm)