Bio::Tools::Run::Phylo::Phylip Neighbor
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Summary
Bio::Tools::Run::Phylo::Phylip::Neighbor - Wrapper for the phylip
program neighbor by Joseph Felsenstein for creating a phylogenetic
tree(either through Neighbor or UPGMA) based on protein distances
based on amino substitution rate.
14 Nov 2002 Shawn
Works with Phylip version 3.6
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 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 neighbor, you # will need to modify the neighbor source code $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params); my $matrix = $protdist_factory->run($aln); #Create the tree passing in the distance matrix @params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1, 'upptri'=>1,'subrep'=>1); my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params); #you can set your outgroup using either a number specifying #the rank in the matrix or you can just use the name of the #species $neighbor_factory->outgroup('ENSP00001'); #or $neighbor_factory->outgroup(1); my ($tree) = $neighbor_factory->run($matrix); # Alternatively, one can create the tree by passing in a file name # containing a phylip formatted distance matrix(using protdist) my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params); my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist'); # To prevent PHYLIP from truncating sequence names: # Step 1. Shelf the original names: my ($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 = $protdist_factory-> creat_distance_matrix($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
No description!
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
new
No description
Code
AUTOLOAD
No description
Code
idlengthDescriptionCode
runDescriptionCode
create_treeDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_input_nbr
No description
Code
namesDescriptionCode
_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.dist';
$tree = $neighborfactory->run($inputfilename);
or
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
$matrix = $protdist_factory->create_distance_matrix($aln);
$tree= $neighborfactory->run($matrix);
Function: a Bio:Tree from a protein distance matrix created by protidst Example : Returns : Bio::Tree Args : Name of a file containing a protein distance matrix in Phylip format or a hash ref to a matrix Throws an exception if argument is not either a string (eg a filename) or a Hash. If argument is string, throws exception if file corresponding to string name can not be found.
create_treecodeprevnextTop
 Title   : create_tree
Usage : my $file = $app->create_tree($treefile);
Function: This method is deprecated. Please use run method.
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
_runcodeprevnextTop
 Title   :  _run
Usage : Internal function, not to be called directly
Function: makes actual system call to neighbor program
Example :
Returns : Bio::Tree object
Args : Name of a file containing protein distances in Phylip format
and a parameter string to be passed to neighbor
_setinput()codeprevnextTop
 Title   : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for neighbor program
Example :
Returns : name of file containing the protein distance matrix in Phylip format
Args : name of file created by protdist or ref to hash created by
Bio::Tools:Run::Phylo::Phylip::ProtDist
names()codeprevnextTop
 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()codeprevnextTop
 Title   :  _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for neighbor program
Example :
Returns : parameter string to be passed to neighbor
Args : name of calling object
Methods code
BEGINTop
BEGIN {
    $PROGRAMNAME="neighbor";
    if (defined $ENV{PHYLIPDIR}) {
	$PROGRAMDIR = $ENV{PHYLIPDIR} || '';
	$PROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,
					  $PROGRAMNAME.($^O =~ /mswin/i ?'.exe':''));
    }
    else {
	$PROGRAM = $PROGRAMNAME;
    }
	@NEIGHBOR_PARAMS = qw(TYPE OUTGROUP LOWTRI UPPTRI SUBREP JUMBLE MULTIPLE);
	@OTHER_SWITCHES = qw(QUIET);
	foreach my $attr(@NEIGHBOR_PARAMS,@OTHER_SWITCHES) {
		$OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
  return 'neighbor';
}
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); } if (! defined $self->idlength){ $self->idlength(10); } 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,$input) = @_;
    my ($temp,$infilename, $seq);
    my ($attr, $value, $switch);
# Create input file pointer
$infilename = $self->_setinput($input); if (!$infilename) {$self->throw("Problems setting up for neighbor. Probably bad input data in $input !");} # Create parameter string to pass to neighbor program
my $param_string = $self->_setparams(); # run neighbor
my @tree = $self->_run($infilename,$param_string); return wantarray ? @tree:\@ tree;
}
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($self->tempdir);
	#open a pipe to run neighbor to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) { open(NEIGHBOR,"|".$self->executable.">/dev/null"); } else { open(NEIGHBOR,"|".$self->executable); } print NEIGHBOR $instring; close(NEIGHBOR); chdir($curpath); #get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile); my $treefile = $self->io->catfile($self->tempdir,$self->treefile); $self->throw("neighbor did not create tree correctly (expected $treefile) ") unless (-e $treefile); my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick'); my @tree; while (my $tree = $in->next_tree){ push @tree, $tree; } # Clean up the temporary files created along the way...
unless ( $self->save_tempfiles ) { unlink $outfile; unlink $treefile; } return @tree;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self, $input) = @_;
    my ($alnfilename,$infilename, $temp, $tfh,$input_tmp,$input_fh);

    #If $input is not a  filename it better be a HASF reference 
# a phy formatted alignment file created by protdist
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); ($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir); my $input_count = 0; foreach my $input(@input){ if ($input->isa("Bio::Matrix::PhylipDist")){ # Open temporary file for both reading & writing of distance matrix
print $tfh $input->print_matrix; $input_count++; } } $self->_input_nbr($input_count); close($tfh); #get names from the first matrix, to be used in outgroup ordering
my %names; $input = shift @input; #set the species names
my @names = @{$input->names}; for(my $i=0; $i<= $#names; $i++){ $names{$names[$i]} = $i+1; } $self->names(\%names); return $alnfilename;
}
_input_nbrdescriptionprevnextTop
sub _input_nbr {
    my ($self,$val) = @_;
    if($val){
        $self->{'_input_nbr'} = $val;
    }    return $self->{'_input_nbr'};
}
namesdescriptionprevnextTop
sub names {
    my ($self,$name) = @_;
    if($name){
        $self->{'_names'} = $name;
    }
    return $self->{'_names'};
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
$self = shift; my $param_string = ""; my $type =""; my $version = $self->version; my %menu = %{$Menu{$version}->{'NEIGHBOR'}}; foreach my $attr ( @NEIGHBOR_PARAMS) { $value = $self->$attr(); next unless (defined $value && $value); if ($attr =~/TYPE/i){ if ($value=~/UPGMA/i){ $type = "UPGMA"; $param_string .= $menu{'TYPE'}{'UPGMA'}; } } elsif($attr =~ /OUTGROUP/i){ if ($type ne "UPGMA"){ if($value !~/^\d+$/){ # is a name so find the rank
my %names = %{$self->names}; $names{$value} || $self->throw("Outgroup $value not found"); $value = $names{$value}; } $param_string .= $menu{'OUTGROUP'}."$value\n"; } else { $self->throw("Can't set outgroup using UPGMA. Use Neighbor-Joining instead"); } } elsif ($attr =~ /JUMBLE/i){ $self->throw("Unallowed value for random seed, need odd number") unless ($value =~ /\d+/ && ($value % 2 == 1)); $param_string .=$menu{'JUMBLE'}."$value\n"; } elsif($attr=~/MULTIPLE/i){ $param_string.=$menu{'MULTIPLE'}."$value\n"; #version 3.6 needs a random seed
if($version eq "3.6"){ $param_string .= (2 * int(rand(10000)) + 1)."\n"; } } else{ $param_string .= $menu{uc $attr}; } } if (($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
PARAMTERS FOR NEIGHBOR COMPUTATIONTop
TYPETop
  Title 	: TYPE
Description : (optional)
This sets the type of tree to construct, using
neighbor joining or UPGMA.
NJ Neighbor Joining UPGMA UPGMA Usage : @params = ('type'=>'X');#where X is one of the values above Defaults to NJ For more information on the usage of the different models, please refer to the documentation found in the phylip package.
OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)Top
  Title		: OUTGROUP 
Description : (optional)
This option selects the species to be used as the outgroup
Acceptable Values: integer
Usage : @params = ('outgroup'=>'X');
where X is an positive integer not more than the
number of sequences
Defaults to 1
LOWTRITop
  Title		: LOWTRI
Description : (optional)
This indicates that the distance matrix is
input in Lower-triangular form (the lower-left
half of the distance matrix only, without the zero
diagonal elements)
Usage : @params = ('lowtri'=>'X'); where X is either 1 or 0
Defaults to 0
UPPTRITop
  Title         : UPPTRI 
Description : (optional)
This indicates that the distance matrix is input in
upper-triangular form (the upper-right half of the
distance matrix only, without the zero diagonal elements.)
Usage : @params = ('upptri'=>'X'); where X is either 1 or 0
Defaults to 0
SUBREPTop
  Title         : SUBREP 
Description : (optional)
This is the Subreplication option.
It informs the program that after each distance will be provided an integer indicating that the distance is a mean of that many replicates. Usage : @params = ('subrep'=>'X'); where X is either 1 or 0 Defaults to 0
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. 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: Usage : @params = ('jumble'=>'17); where 17 is the random seed Defaults to no jumble
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.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
outfileTop
 Title   : outfile
Usage : $obj->outfile($newval)
Function: Get/Set default PHYLIP outfile name ('outfile' usually)
Returns : value of outfile
Args : newvalue (optional)
treefileTop
 Title   : treefile
Usage : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args : newvalue (optional)