Bio::Tools::Run::Phylo::Phylip::Consense.3pm

Langue: en

Autres versions - même langue

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::Phylo::Phylip::Consense - Wrapper for the phylip program Consense

SYNOPSIS

   use Bio::Tools::Run::Phylo::Phylip::Consense;
   use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
   use Bio::Tools::Run::Phylo::Phylip::ProtDist;
   use Bio::Tools::Run::Phylo::Phylip::Neighbor;
   use Bio::Tools::Run::Phylo::Phylip::DrawTree;
 
 
   #first get an alignment
   my $aio= Bio::AlignIO->new(-file=>$ARGV[0],-format=>"clustalw");
   my $aln = $aio->next_aln;
 
   # To prevent truncation of sequence names by PHYLIP runs, use set_displayname_safe
   my ($aln_safe, $ref_name)=$aln->set_displayname_safe();
 
   #next use seqboot to generate multiple aligments
   my @params = ('datatype'=>'SEQUENCE','replicates'=>10);
   my $seqboot_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);
 
   my $aln_ref= $seqboot_factory->run($aln);
 
   Or, for long sequence names:
 
   my $aln_ref= $seqboot_factory->run($aln_safe);
 
   #next build distance matrices and construct trees
   my $pd_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
   my $ne_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
 
   foreach my $a (@{$aln_ref}){
     my $mat = $pd_factory->create_distance_matrix($a);
     push @tree, $ne_factory->create_tree($mat);
   }
 
   #now use consense to get a final tree
   my $con_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();
 
   #you may set outgroup either by the number representing the order in
   #which species are entered or by the name of the species
 
   $con_factory->outgroup(1);
   $con_factory->outgroup('HUMAN');
 
   my $tree = $con_factory->run(\@tree);
 
   # Restore original sequence names, after ALL phylip runs:
   my @nodes = $tree->get_nodes();
   foreach my $nd (@nodes){
      $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
   }
 
   #now draw the tree
   my $draw_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
   my $image_filename = $draw_factory->draw_tree($tree);

DESCRIPTION

Wrapper for phylip consense program

Taken from phylip documentation...

CONSENSE reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree. At the moment it carries out a family of consensus tree methods called the M[l] methods (Margush and McMorris, 1981). These include strict consensus and majority rule consensus. Basically the consensus tree consists of monophyletic groups that occur as often as possible in the data.

More documentation on using Consense and setting parameters may be found in the phylip package.

VERSION Support

This wrapper currently supports v3.5 of phylip. There is also support for v3.6 although this is still experimental as v3.6 is still under alpha release and not all functionalities maybe supported.

PARAMETERS FOR Consense

TYPE

Title         : TYPE
Description     : (optional)

             Only avaliable in phylip v3.6 
                   This program supports 3 types of consensus generation 
 
                   MRe   : Majority Rule (extended) Any set of species that
                           appears in more than 50% of the trees is included. 
                           The program then considers the other sets of species 
                           in order of the frequency with which they have appeared, 
                           adding to the consensus tree any which are compatible 
                           with it until
 
                   STRICT: A set of species must appear in all input trees to be 
                           included in the strict consensus tree. 
 
                   MR    :  A set of species is included in the consensus tree 
                           if it is present in more than half of the input trees. 
 
                   Ml    : The user is asked for a fraction between 0.5 and 1, and 
                           the program then includes in the consensus tree any set 
                           of species that occurs among the input trees more than 
                           that fraction of then time. The Strict consensus and the 
                           Majority Rule consensus are extreme cases of the M[l] consensus,
                           being for fractions of 1 and 0.5 respectively
 
                   usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-type=>"Ml 0.7");
 
 
              Defaults to MRe

ROOTED

   Title: ROOTED 
   Description: (optional)
 
              toggles between the default assumption that the input trees are unrooted trees and 
              the selection that specifies that the tree is to be treated as a rooted tree and not 
              re-rooted. Otherwise the tree will be treated as outgroup-rooted and will be
              re-rooted automatically at the first species encountered on the first tree 
              (or at a species designated by the Outgroup option)
 
              usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-rooted=>1);
 
              Defaults to unrooted

OUTGROUP

   Title         : OUTGROUP
   Description   : (optional)
 
                 It is in effect only if the Rooted option selection is not in effect.
                 The trees will be re-rooted with a species of your choosing.
 
                 usage  my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-outgroup=>2);
 
                 Defaults to first species encountered.

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 - Shawn Hoon

Email shawnh@fugu-sg.org

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    :

idlength

  Title   : idlength 
  Usage   : $obj->idlength ($newval)
  Function: 
  Returns : value of idlength 
  Args    : newvalue (optional)

run

  Title   : run 
  Usage   :
         $inputfilename = 't/data/prot.treefile';
         $tree= $Consense_factory->run($inputfilename);
 or
 
         $tree= $consense_factory->run(\@tree);
 
  Function: Create bootstrap sets of alignments
  Example :
  Returns : a L<Bio::Tree::Tree>
  Args    : either a file containing trees in newick format
            or an array ref of L<Bio::Tree::Tree>
 
  Throws an exception if argument is not either a string (eg a
  filename) or a Bio::Tree::TreeI object. If
  argument is string, throws exception if file corresponding to string
  name can not be found.

_run

  Title   :  _run
  Usage   :  Internal function, not to be called directly        
  Function:  makes actual system call to Consense program
  Example :
  Returns : an array ref of <Bio::Tree::Tree> 
  Args    : Name of a file containing a set of tree in newick format 
            and a parameter string to be passed to Consense

_setinput()

  Title   :  _setinput
  Usage   :  Internal function, not to be called directly        
  Function:   Create input file for Consense program
  Example :
  Returns : name of file containing a trees in newick format
  Args    : an array ref of Bio::Tree::Tree object or input file name

names()

  Title   :  names
  Usage   :  $tree->names(\%names)
  Function:  get/set for a hash ref for storing names in matrix
             with rank as values.
  Example :
  Returns : hash reference
  Args    : hash reference

_setparams()

  Title   :  _setparams
  Usage   :  Internal function, not to be called directly        
  Function:   Create parameter inputs for Consense program
  Example :
  Returns : parameter string to be passed to Consense
  Args    : name of calling object

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 = $Consense->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   : $codeml->cleanup();
  Function: Will cleanup the tempdir directory after a Consense 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