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

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   #Create a SimpleAlign object
   @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
   $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
   $inputfilename = 't/data/cysprot.fa';
   $aln = $factory->run($inputfilename); # $aln is a SimpleAlign object.
 
 
   # Create the Distance Matrix using a default PAM matrix and id name
   # lengths limit of 30 note to use id name length greater than the
   # standard 10 in protdist, you will need to modify the protdist source
   # code
 
   @params = ('MODEL' => 'PAM');
   $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
 
   my ($matrix)  = $protdist_factory->run($aln); # an array of Bio::Matrix::PhylipDist matrix
 
   #finding the distance between two sequences
   my $distance = $matrix->get_entry('protein_name_1','protein_name_2');
   my @column   = $matrix->get_column('protein_name_1');
   my @row      = $martrix->get_row('protein_name_1');
   my @diag     = $matrix->get_diagonal();
   print $matrix->print_matrix;
 
 
   #Alternatively, one can create the matrix by passing in a file 
   #name containing a multiple alignment in phylip format
   $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
   my ($matrix)  = $protdist_factory->run('/home/shawnh/prot.phy');
 
   # To prevent PHYLIP from truncating sequence names:
   # Step 1. Shelf the original names:
     my ($aln_safe, $ref_name)=                    #   $aln_safe has serial names
                $aln->set_displayname_safe();      #   $ref_name holds original names
   # Step 2. Run ProtDist and Neighbor:
     ($matrix) = $protdist_factory->
                create_distance_matrix($aln_safe); #  Use $aln_safe instead of $aln
     ($tree) = $neighbor_factory->run($matrix);
   # Step 3. Retrieve orgininal OTU names:
     use Bio::Tree::Tree;
     my @nodes=$tree->get_nodes();
     foreach my $nd (@nodes){
        $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
     }
 
 

DESCRIPTION

Wrapper for protdist Joseph Felsentein for creating a distance matrix comparing protein sequences from a multiple alignment file or a Bio::SimpleAlign object and returns a Bio::Matrix::PhylipDist object;

VERSION Support

This wrapper currently supports v3.5 of phylip. There is also support for v3.6.

PARAMETERS FOR PROTDIST COMPUTATION

MODEL

Title         : MODEL
Description     : (optional)
                   This sets the model of amino acid substitution used
                   in the calculation of the distances.  3 different
                   models are supported: 
                   PAM     Dayhoff PAM Matrix(default) 
                   KIMURA  Kimura's Distance CAT
 
                   Categories Distance Usage: @params =
                   ('model'=>'X');#where X is one of the values above
 
                   Defaults to PAM For more information on the usage of
                   the different models, please refer to the
                   documentation 
                   defaults to Equal
                   (0.25,0.25,0.25,0.25) found in the phylip package.
 
                   Additional models in PHYLIP 3.6
                   PMB - Henikoff/Tillier PMB matrix
                   JTT - Jones/Taylor/Thornton
 
 

MULTIPLE

Title : MULTIPLE Description: (optional)
           This allows multiple distance matrices to be generated from multiple
           MSA.
 
           Usage: @params = ('MULTIPLE'=>100) where the value specifyies the 
           number of aligments given.
 
 

ALL SUBSEQUENT PARAMETERS WILL ONLY WORK IN CONJUNCTION WITH

THE Categories Distance MODEL*

GENCODE

   Title         : GENCODE 
   Description   : (optional)
 
                   This option allows the user to select among various
                   nuclear and mitochondrial genetic codes.
 
                   Acceptable Values:
                   U           Universal
                   M           Mitochondrial
                   V           Vertebrate mitochondrial
                   F           Fly mitochondrial
                   Y           Yeast mitochondrial
   Usage         : @params = ('gencode'=>'X'); 
                   where X is one of the letters above
                   Defaults to U
 
 

CATEGORY

Title         : CATEGORY
Description : (optional)
                   This option sets the categorization of amino acids
                   all have groups: (Glu Gln Asp Asn), (Lys Arg His),
                   (Phe Tyr Trp)  plus:
                   G   George/Hunt/Barker:
                           (Cys), (Met   Val  Leu  Ileu), 
                           (Gly  Ala  Ser  Thr  Pro)
                   C   Chemical:
                           (Cys   Met), (Val  Leu  Ileu  Gly  Ala  Ser  Thr),
                           (Pro)
                   H   Hall:
                         (Cys), (Met   Val  Leu  Ileu), (Gly  Ala  Ser  Thr),
                         (Pro)
 
   Usage         : @params = ('category'=>'X'); 
                   where X is one of the letters above
                   Defaults to G
 
 

PROBCHANGE

   Title       : PROBCHANGE
   Description : (optional)
                  This option sets the ease of changing category of amino
                  acid.  (1.0 if no difficulty of changing,less if less
                  easy. Can't be negative)
 
   Usage       : @params = ('probchange'=>X) where 0<=X<=1
                 Defaults to 0.4570
 
 

TRANS

   Title       : TRANS
   Description : (optional)
                 This option sets transition/transversion ratio can be
                 any positive number
 
   Usage        : @params = ('trans'=>X) where X >= 0
                  Defaults to 2
 
 

FREQ

   Title       : FREQ 
   Description : (optional)
                 This option sets the frequency of each base (A,C,G,T)
                 The sum of the frequency must sum to 1.
                 For example A,C,G,T = (0.25,0.5,0.125,0.125) 
 
   Usage       : @params = ('freq'=>('W','X','Y','Z')
                 where W + X + Y + Z = 1
                 Defaults to Equal (0.25,0.25,0.25,0.25)
 
 

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   : >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.phy';
         $matrix= $prodistfactory->run($inputfilename);
 or
         $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
         $aln = $protdistfactory->align($seq_array_ref);
         $matrix = $protdistfactory->run($aln);
 
  Function: Create a distance matrix from a SimpleAlign object or a multiple alignment file 
  Example :
  Returns : L<Bio::Matrix::PhylipDist>
  Args    : Name of a file containing a multiple alignment in Phylip format
            or an SimpleAlign object 
 
  Throws an exception if argument is not either a string (eg a
  filename) or a Bio::SimpleAlign 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 protdist program
  Example :
  Returns : Bio::Tree object
  Args    : Name of a file containing a set of multiple alignments in Phylip format 
            and a parameter string to be passed to protdist
 
 

create_distance_matrix

  Title   : create_distance_matrix
  Usage   : my $file = $app->create_distance_matrix($treefile);
  Function: This method is deprecated. Please use run method. 
  Returns : L<Bio::Matrix::PhylipDist>
  Args    : Name of a file containing a multiple alignment in Phylip format
            or an SimpleAlign object 
 
  Throws an exception if argument is not either a string (eg a
  filename) or a Bio::SimpleAlign object. If
  argument is string, throws exception if file corresponding to string
  name can not be found.
 
 

_setinput()

  Title   :  _setinput
  Usage   :  Internal function, not to be called directly        
  Function:   Create input file for protdist program
  Example :
  Returns : name of file containing a multiple alignment in Phylip format 
  Args    : SimpleAlign object reference or input file name
 
 

_setparams()

  Title   :  _setparams
  Usage   :  Internal function, not to be called directly        
  Function:   Create parameter inputs for protdist program
  Example :
  Returns : parameter string to be passed to protdist
  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 = $protdist->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 ProtDist 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