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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://bugzilla.open-bio.org/
 
 

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