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