Bio::Tools::Run::Phylo::Phylip ProtPars
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Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::IO
Bio::Root::Root
Bio::SimpleAlign
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 Tree #using a threshold value of 30 and id name lengths limit of 30 #note to use id name length greater than the standard 10 in protpars, # you will need to modify the protpars source code $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars-> new(idlength=>30,threshold=>10,jumble=>"17,10",outgroup=>2); $tree = $tree_factory->run($aln); #Or one can pass in a file name containing a multiple alignment #in phylip format: $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10); $tree = $tree_factory->run("/usr/users/shawnh/COMPARA/prot.phy"); # To prevent PHYLIP from truncating sequence names: # Step 1. Shelf the original names: my ($aln_safe, $ref_name)= # $aln_safe has serial names $aln->set_displayname_safe(); # $ref_name holds original names # Step 2. Run ProtPars: $tree = $protpars_factory->run($aln_safe); # Use $aln_safe instead of $aln # Step 3. Retrieve orgininal OTU names: use Bio::Tree::Tree; my @nodes=$tree->get_nodes(); foreach my $nd (@nodes){ $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf; }
Description
No description!
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
idlengthDescriptionCode
runDescriptionCode
create_treeDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_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';
$tree = $factory->run($inputfilename);
or
$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $factory->run($seq_array_ref);
$tree = $treefactory->run($aln);
Function: Create a protpars tree from a SimpleAlign object
Example :
Returns : Bio::Tree object
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.
create_tree codeprevnextTop
 Title   : create_tree 
Usage :
$inputfilename = 't/data/prot.phy';
$tree = $factory->create_tree($inputfilename);
or
$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $factory->align($seq_array_ref);
$tree = $treefactory->create_tree($aln);
Function: Create a protpars tree from a SimpleAlign object
Example :
Returns : Bio::Tree object
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 protpars 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 protpars
_setinput()codeprevnextTop
 Title   :  _setinput
Usage : Internal function, not to be called directly
Function: Create input file for protpars 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 protpars program
Example :
Returns : parameter string to be passed to protpars
Args : name of calling object
Methods code
BEGINTop
BEGIN {
    @PROTPARS_PARAMS = qw(THRESHOLD JUMBLE OUTGROUP);
    @OTHER_SWITCHES = qw(QUIET);
    foreach my $attr(@PROTPARS_PARAMS,@OTHER_SWITCHES) {
	$OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
            return 'protpars';
}
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 =~ /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 protpars. Probably bad input data in $input !");} # Create parameter string to pass to protpars program
my $param_string = $self->_setparams(); # run protpars
my $aln = $self->_run($infilename,$param_string);
}
create_treedescriptionprevnextTop
sub create_tree {
  return shift->run(@_);
}

#################################################
}
_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."\n");
    chdir($self->tempdir);
    #open a pipe to run protpars to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) { open(PROTPARS,"|".$self->executable.">/dev/null"); } else { open(PROTPARS,"|".$self->executable); } print PROTPARS $instring; close(PROTPARS); chdir($curpath); #get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile); my $treefile = $self->io->catfile($self->tempdir,$self->treefile); $self->throw("Protpars did not create treefile correctly") unless (-e $treefile); #create the tree
my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick'); my $tree = $in->next_tree(); unless ( $self->save_tempfiles ) { # Clean up the temporary files created along the way...
unlink $treefile; unlink $outfile; } return $tree;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self, $input, $suffix) = @_;
    my ($alnfilename,$infilename, $temp, $tfh,$input_tmp,$input_fh);

    # 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; } # $input may be a SimpleAlign Object
if ($input->isa("Bio::Align::AlignI")) { # Open temporary file for both reading & writing of BioSeq array
($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir); my $alnIO = Bio::AlignIO->new(-fh => $tfh, -format=>'phylip',idlength=>$self->idlength()); $alnIO->write_aln($input); $alnIO->close(); close($tfh); $tfh = undef; return $alnfilename; } return 0;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($attr, $value, $self);

    $self = shift;
    my $param_string = "";
    
    my %menu = %{$Menu{$self->version}->{'PROTPARS'}};

    for $attr ( @PROTPARS_PARAMS) {
        $value = $self->$attr();
        next unless (defined $value);
	      if ($attr =~/JUMBLE/i){
      		my ($seed,$itr) = split(",",$value);
      		$param_string .=$menu{'JUMBLE'}."$seed\n$itr\n";
      	}
        else {
          $param_string .= $menu{uc $attr}."$value\n";
        }
    } 
    $param_string .="Y\n";

    return $param_string;
}

1; # Needed to keep compiler happy
}
General documentation
NAME Top
Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
14 Nov 2002 Shawn
Works with Phylip version 3.6
PARAMTERS FOR PROTPARS COMPUTATIONTop
THRESHOLDTop
Title : THRESHOLD
Description : (optional)
This sets a threshold such that if the number of
steps counted in a character is higher than the
threshold, it will be taken to be the threshold
value rather than the actual number of steps. You
should use a positive real number greater than 1.
Please see the documetation from the phylip package
for more information.
OUTGROUPTop
Title : OUTGROUP
Description : (optional)
                  This specifies which species is to be used to root
the tree by having it become the outgroup. Input
values are integers specifying which species to use.
Defaults to 1
JUMBLETop
Title : JUMBLE
Description : (optional)
This enables you to tell the program to use a random
number generator to choose the input order of
species. Input values is of the format:
seed,iterations eg 17,10 seed: an integer between 1
and 32767 and of the form 4n+1 which means that it
must give a remainder of 1 when divided by 4. Each
different seed leads to a different sequence of
addition of species. By simply changing the random
number seed and re-running programs one can look for
other, and better trees. iterations: For a value of
10, this will tell the program to try ten different
orders of species in constructing the trees, and the
results printed out will reflect this entire search
process (that is, the best trees found among all 10
runs will be printed out, not the best trees from
each individual run).
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
CONTRIBUTORSTop
Email jason-AT-bioperl_DOT_org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _