Bio::Tools::Run::Phylo::Phylip ProtDist
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Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::SimpleAlign
Bio::Tools::Phylo::Phylip::ProtDist
Bio::Tools::Run::Phylo::Phylip::Base
Bio::Tools::Run::Phylo::Phylip::PhylipConf qw ( %Menu )
Bio::TreeIO
Cwd
Inherit
Bio::Tools::Run::Phylo::Phylip::Base
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.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
idlengthDescriptionCode
runDescriptionCode
_runDescriptionCode
create_distance_matrixDescriptionCode
_setinputDescriptionCode
_input_nbr
No description
Code
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : >program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
idlength codeprevnextTop
 Title   : idlength 
Usage : $obj->idlength ($newval)
Function:
Returns : value of idlength
Args : newvalue (optional)
run codeprevnextTop
 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 : 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.
_runcodeprevnextTop
 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_matrixcodeprevnextTop
 Title   : create_distance_matrix
Usage : my $file = $app->create_distance_matrix($treefile);
Function: This method is deprecated. Please use run method.
Returns : 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()codeprevnextTop
 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()codeprevnextTop
 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
Methods code
BEGINTop
BEGIN {
	@PROTDIST_PARAMS = qw(MODEL GENCODE CATEGORY PROBCHANGE TRANS WEIGHTS FREQ MULTIPLE);
	@OTHER_SWITCHES = qw(QUIET);
	foreach my $attr(@PROTDIST_PARAMS,@OTHER_SWITCHES) {
		$OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
  return 'protdist';
}
program_dirdescriptionprevnextTop
sub program_dir {
  return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);    
    my ($attr, $value);
    while (@args)  {
	$attr =   shift @args;
	$value =  shift @args;
	next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) { $self->executable($value); next; } if ($attr =~ /IDLENGTH/i){ $self->idlength($value); next; } $self->$attr($value); } return $self;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};
}
idlengthdescriptionprevnextTop
sub idlength {
   my $self = shift;
   if( @_ ) {
      my $value = shift;
      $self->{'idlength'} = $value;
    }
    return $self->{'idlength'};
}
rundescriptionprevnextTop
sub run {
    my ($self,$input) = @_;
    my ($infilename);

 # Create input file pointer
$infilename = $self->_setinput($input); if (!$infilename) {$self->throw("Problems setting up for protdist. Probably bad input data in $input !");} # Create parameter string to pass to protdist program
my $param_string = $self->_setparams(); # run protdist
my @mat = $self->_run($infilename,$param_string); return wantarray ? @mat:\@mat; } #################################################
}
_rundescriptionprevnextTop
sub _run {
    my ($self,$infile,$param_string) = @_;
    my $instring;
    my $curpath = cwd;    
    unless( File::Spec->file_name_is_absolute($infile) ) {
	$infile = $self->io->catfile($curpath,$infile);
    }
    $instring =  $infile."\n$param_string";
    $self->debug( "Program ".$self->executable." $instring\n");
    
    chdir($self->tempdir);
    #open a pipe to run protdist to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) { open(PROTDIST,"|".$self->executable .">/dev/null"); } else { open(PROTDIST,"|".$self->executable); } print PROTDIST $instring; close(PROTDIST); # get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile); chdir($curpath); $self->throw("protdist did not create matrix correctly ($outfile)") unless (-e $outfile); #Create the distance matrix here
my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-file=>$outfile); my @matrix; while (my $mat = $parser->next_matrix){ push @matrix, $mat; } # Clean up the temporary files created along the way...
unlink $outfile unless $self->save_tempfiles; return @matrix;
}
create_distance_matrixdescriptionprevnextTop
sub create_distance_matrix {
  return shift->run(@_);
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self, $input) = @_;
    my ($alnfilename,$tfh);

    # suffix is used to distinguish alignment files  from an align obkect
#If $input is not a reference it better be the name of a file with the sequence/
# a phy formatted alignment file
unless (ref $input) { # check that file exists or throw
$alnfilename= $input; unless (-e $input) {return 0;} return $alnfilename; } my @input = ref $input eq 'ARRAY' ? @{$input} : ($input); # $input may be a SimpleAlign Object
($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir); my $alnIO = Bio::AlignIO->new(-fh => $tfh, -format=>'phylip', -idlength=>$self->idlength()); my $input_count = 0; foreach my $input(@input){ if ($input->isa("Bio::SimpleAlign")){ # Open temporary file for both reading & writing of BioSeq array
$alnIO->write_aln($input); } $input_count++; } $alnIO->close(); close($tfh); $tfh = undef; $self->_input_nbr($input_count); return $alnfilename;
}
_input_nbrdescriptionprevnextTop
sub _input_nbr {
    my ($self,$val) = @_;
    if($val){
        $self->{'_input_nbr'} = $val;
    }
    return $self->{'_input_nbr'};
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
$self = shift; my $param_string = ""; my $cat = 0; my %menu = %{$Menu{$self->version}->{'PROTDIST'}}; foreach my $attr ( @PROTDIST_PARAMS) { $value = $self->$attr(); next unless (defined $value); if ($attr =~/MODEL/i){ if ($value=~/CAT/i){ $cat = 1; } $param_string .= $menu{'MODEL'}{$value}; } if($attr=~/MULTIPLE/i){ $param_string.=$menu{'MULTIPLE'}."$value\n"; } if ($cat == 1){ if($attr =~ /GENCODE/i){ my $allowed = $menu{'GENCODE'}{'ALLOWED'}; $self->throw("Unallowed value for genetic code") unless ($value =~ /[$allowed]/); $param_string .= $menu{'GENCODE'}{'OPTION'}."$value\n"; } if ($attr =~/CATEGORY/i){ my $allowed = $menu{'CATEGORY'}{'ALLOWED'}; $self->throw("Unallowed value for categorization of amino acids") unless ($value =~/[$allowed]/); $param_string .= $menu{'CATEGORY'}{'OPTION'}."$value\n"; } if ($attr =~/PROBCHANGE/i){ if (($value =~ /\d+/)&&($value >= 0) && ($value < 1)){ $param_string .= $menu{'PROBCHANGE'}."$value\n"; } else { $self->throw("Unallowed value for probability change category"); } } if ($attr =~/TRANS/i){ if (($value=~/\d+/) && ($value >=0)){ $param_string .=$menu{'TRANS'}."$value\n"; } } if ($attr =~ /FREQ/i){ my @freq = split(",",$value); if ($freq[0] !~ /\d+/){ #a letter provided (sets frequencies equally to 0.25)
$param_string .=$menu{'FREQ'}.$freq[0]."\n"; } elsif ($#freq == 3) {#must have 4 digits for each base
$param_string .=$menu{'FREQ'}; foreach my $f (@freq){ $param_string.="$f\n"; } } else { $self->throw("Unallowed value for base frequencies"); } } } } #set multiple option is not set and there are more than one sequence
if (($param_string !~ $menu{'MULTIPLE'}) && (defined ($self->_input_nbr) &&($self->_input_nbr > 1))){ $param_string.=$menu{'MULTIPLE'}.$self->_input_nbr."\n"; } $param_string .=$menu{'SUBMIT'}; return $param_string;
}
General documentation
NAME Top
Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip
program protdist
PARAMETERS FOR PROTDIST COMPUTATIONTop
MODELTop
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
MULTIPLETop
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 WITHTop
THE Categories Distance MODEL*
GENCODETop
  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
CATEGORYTop
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
PROBCHANGETop
  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 Top
  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
FREQTop
  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)
FEEDBACKTop
Mailing ListsTop
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 Top
 
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 BugsTop
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 Top
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::Tools::Run::Wrapper methodsTop
no_param_checksTop
 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_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_nameTop
 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
tempdirTop
 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
cleanupTop
 Title   : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a ProtDist run
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none