/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Phylip::ProtDist

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://redmine.open-bio.org/projects/bioperl/

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