Bio::Tools::Run::Phylo::PAML::Baseml.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml

SYNOPSIS

   use Bio::Tools::Run::Phylo::PAML::Baseml;
   use Bio::AlignIO;
   my $alignio = Bio::AlignIO->new(-format => 'phylip',
                                  -file   => 't/data/gf-s85.phylip');
   my $aln = $alignio->next_aln;
 
   my $bml = Bio::Tools::Run::Phylo::PAML::Baseml->new();
   $bml->alignment($aln);
   my ($rc,$parser) = $bml->run();
   while( my $result = $parser->next_result ) {
     my @otus = $result->get_seqs();
     my $MLmatrix = $result->get_MLmatrix();
     # 0 and 1 correspond to the 1st and 2nd entry in the @otus array
   }
 
 

DESCRIPTION

This is a wrapper around the baseml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information.

This module will generate a proper baseml.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself..

The values you can feed to the configuration file are documented here.

     'noisy'   => [ 0..3,9],
     'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much
     'runmode' => [0..5], 
     # for runmode
     # 0: use the provided tree structure(s) in treefile
     # 1,2: mean heuristic search by star-decomposition alg
     # 2: starts from star tree while 1 reads a multifurcating 
     # tree from treefile and ties to estimate the best 
     # bifurcating tree
     # 3: stepwise addition
     # 4: NNI perturbation with the starting tree
     # Tree search DOES NOT WORK WELL so estimate a tree
     # using other programs first
     'model'   => '0', 
     # for model
     # 0: JC69 (uncorrected)
     # 1: K80  (transitions/transversion weighted differently)
     # 2: F81
     # 3: F84
     # 4: HKY85
     # 5: T92 (Tamura 92) 
     # 6: TN93 (Tajima-Nei) correct for multiple substitutions
     # 7: REV (aka GTR)
     # 8: UNREST 
     # 9: REVu
     #10: UNRESTu
     # See Yang 1994 JME 39:105-111
 
     # model 8 special case of the REV model
     # model 9 is special case of unrestricted model
     # can also supply special rate parameters
     # so for example (from pamlDOC.pdf
     # $model  = '8 [2 (CT) (AG)]'; # TN93 
     # $model  = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93
     # $model  = '9 [1 (TC CT AG GA)]; # K80
     # $model  = '9 [0]'; # JC69
     # $model  = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)],
 
     'outfile' => 'mlb',
     'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa
     'kappa'    => '2.5', # initial or fixed kappa
     'fix_alpha'=> [1,0], # 0: estimate gamma shape param
     # 1: fix it at alpha
     'alpha'    => '0', # initial of fixed alpha
     # 0: infinity (constant rate)
     'Malpha'   => [0,1], # different alphas for genes
 
     'fix_rho'=> [1,0], # 0: estimate gamma shape param
                                           # 1: fix it at alpha
     'rho'    => '0', # initial of fixed alpha
     # 0: infinity (constant rate)
 
     'ncatG'    => '5', # number of categories in the dD,AdG, or nparkK models of rates
     'nparK'    => [0..4], # rate-class models 
     # 1:rk 2:rk&fK 
     # 3:rK&MK(1/K) 4:rK&MK
     'nhomo'    => [0..4], # 0 & 1: homogeneous,
     # 2: kappa for brances
     # 3:N1 4:N2
     'getSE'    => [0,1],
     'RateAncestor' => [1,0,2], # rates (alpha > 0) or
     # ancestral states
     'cleandata' => [1,0], # remove sites with 
     # ambiguity data (1:yes or 0:no)
 
     'fix_blength' => [-1,0,1,2], # 0: ignore, -1: random,
     # 1: initial, 2: fixed
 
     # 'icode'    => [ 0..10], # (with RateAncestor=1.
     #try "GC" in data,model=4,Mgene=4)
     'ndata'    => [5,1..10],
     'clock'    => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis
     'Small_Diff' => '1e-6', #underflow issues?
 
 

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://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala - 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   : $obj->program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : ->program_dir()
  Function: returns the program directory, obtained from ENV variable.
  Returns:  string
  Args    :
 
 

new

  Title   : new
  Usage   : my $obj = Bio::Tools::Run::Phylo::PAML::Baseml->new();
  Function: Builds a new Bio::Tools::Run::Phylo::PAML::Baseml object 
  Returns : Bio::Tools::Run::Phylo::PAML::Baseml
  Args    : -alignment => the L<Bio::Align::AlignI> object
            -tree => the L<Bio::Tree::TreeI> object if you want to use runmode
                     0 or 1
            -save_tempfiles => boolean to save the generated tempfiles and
                               NOT cleanup after onesself (default FALSE)
 
 

run

  Title   : run
  Usage   : $yn->run();
  Function: run the Baseml analysis using the default or updated parameters
            the alignment parameter must have been set
  Returns : 3 values, 
            $rc = 1 for success, 0 for errors
            hash reference of the Yang calculated Ka/Ks values
                     this is a set of pairwise observations keyed as
                     sequencenameA->sequencenameB->datatype
            hash reference same as the previous one except it for the 
            Nei and Gojobori calculated Ka,Ks,omega values
  Args    : optionally, a value appropriate for alignment() and one for tree()
  NB      : Since Baseml doesn't handle spaces in tree node ids, if a tree is
            in use spaces will be converted to underscores in both the tree node
            ids and alignment sequence ids.
 
 

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)
 
 

alignment

  Title   : alignment
  Usage   : $baseml->alignment($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>
 
 

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
 
 

set_parameter

  Title   : set_parameter
  Usage   : $baseml->set_parameter($param,$val);
  Function: Sets a baseml parameter, will be validated against
            the valid values as set in the %VALIDVALUES class variable.  
            The checks can be ignored if on turns of param checks like this:
              $baseml->no_param_checks(1)
  Returns : boolean if set was success, if verbose is set to -1
            then no warning will be reported
  Args    : $paramname => name of the parameter
            $value     => value to set the parameter to
  See also: L<no_param_checks()>
 
 

set_default_parameters

  Title   : set_default_parameters
  Usage   : $baseml->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
  NB      : using this isn't an especially good idea! You don't need to do
            anything to end up using default paramters: hence 'default'!
 
 

Bio::Tools::Run::Wrapper methods

no_param_checks

  Title   : no_param_checks
  Usage   : $obj->no_param_checks($newval)
  Function: Boolean flag as to whether or not we should
            trust the sanity checks for parameter values  
  Returns : value of no_param_checks
  Args    : newvalue (optional)
 
 

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 = $baseml->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   : $baseml->cleanup();
  Function: Will cleanup the tempdir directory after a PAML run
  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