Bio::Tools::Run::Phylo QuickTree
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Summary
Bio::Tools::Run::Phylo::QuickTree - Wrapper for rapid reconstruction of
phylogenies using QuickTree
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::TreeIO
Inherit
Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Phylo::QuickTree;
# Make a QuickTree factory @params = (); $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params); # Pass the factory an alignment $inputfilename = 't/data/cysprot.stockholm'; $tree = $factory->run($inputfilename); # $tree is a Bio::Tree::Tree object. # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere $tree = $factory->run($aln);
Description
This is a wrapper for running the QuickTree application by Kevin Howe. You
can download it here: http://www.sanger.ac.uk/Software/analysis/quicktree/
Currently only input with alignments and output of trees is supported. (Ie.
no support for distance matrix in/out.)
You will need to enable this QuickTree wrapper to find the quicktree program.
This can be done in (at least) three ways:
 1. Make sure the QuickTree executable is in your path.
2. Define an environmental variable QUICKTREEDIR which is a
directory which contains the 'quicktree' application:
In bash:
export QUICKTREEDIR=/home/username/quicktree_1.1/bin In csh/tcsh: setenv QUICKTREEDIR /home/username/quicktree_1.1/bin 3. Include a definition of an environmental variable QUICKTREEDIR in every script that will use this QuickTree wrapper module, e.g.: BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' } use Bio::Tools::Run::Phylo::QuickTree;
Methods
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
upgmaDescriptionCode
kimuraDescriptionCode
bootDescriptionCode
runDescriptionCode
_run
No description
Code
_setparamsDescriptionCode
_writeAlignFileDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : None
newcodeprevnextTop
 Title   : new
Usage : $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params)
Function: creates a new QuickTree factory
Returns : Bio::Tools::Run::Phylo::QuickTree
Args : Optionally, provide any of the following (default in []):
-upgma => boolean # Use the UPGMA method to construct the tree [0]
-kimura => boolean # Use the kimura translation for pairwise
# distances [0]
-boot => int # Calculate bootstrap values with n iterations [0]
upgmacodeprevnextTop
 Title   : upgma
Usage : $factory->upgma(1);
Function: Choose to use the UPGMA method to construct the tree.
Returns : boolean (default 0)
Args : None to get, boolean to set.
kimuracodeprevnextTop
 Title   : kimura
Usage : $factory->kimura(1);
Function: Choose to use the kimura translation for pairwise distances.
Returns : boolean (default 0)
Args : None to get, boolean to set.
bootcodeprevnextTop
 Title   : boot
Usage : $factory->boot(100);
Function: Choose to calculate bootstrap values with the supplied number of
iterations.
Returns : int (default 0)
Args : None to get, int to set.
runcodeprevnextTop
 Title   : run
Usage : $factory->run($stockholm_file);
$factory->run($align_object);
Function: Runs QuickTree to generate a tree
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in stockholm format, OR
Bio::Align::AlignI complient object (eg. Bio::SimpleAlign).
_setparamscodeprevnextTop
 Title   : _setparams
Usage : Internal function, not to be called directly
Function: Creates a string of params to be used in the command string
Returns : string of params
Args : none
_writeAlignFilecodeprevnextTop
 Title   : _writeAlignFile
Usage : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : Bio::Align::AlignI
Methods code
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAM_NAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
    return $PROGRAM_DIR;
}
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    # for consistency with other run modules, allow params to be dashless
my %args = @args; while (my ($key, $val) = each %args) { if ($key !~ /^-/) { delete $args{$key}; $args{'-'.$key} = $val; } } my ($upgma, $kimura, $boot) = $self->_rearrange([qw(UPGMA KIMURA BOOT)], %args); $self->upgma(1) if $upgma; $self->kimura(1) if $kimura; $self->boot($boot) if $boot; return $self;
}
upgmadescriptionprevnextTop
sub upgma {
    my ($self, $bool) = @_;
    if (defined ($bool)) {
        $self->{upgma} = $bool;
    }
    return $self->{upgma} || 0;
}
kimuradescriptionprevnextTop
sub kimura {
    my ($self, $bool) = @_;
    if (defined ($bool)) {
        $self->{kimura} = $bool;
    }
    return $self->{kimura} || 0;
}
bootdescriptionprevnextTop
sub boot {
    my ($self, $int) = @_;
    if (defined ($int)) {
        $self->{boot} = $int;
    }
    return $self->{boot} || 0;
}
rundescriptionprevnextTop
sub run {
    my ($self, $in) = @_;

    if (ref $in && $in->isa("Bio::Align::AlignI")) {
        $in = $self->_writeAlignFile($in);
    }
    elsif (! -e $in) {
        $self->throw("When not supplying a Bio::Align::AlignI object, you must supply a readable filename");
    }
    
    return $self->_run($in);
}
_rundescriptionprevnextTop
sub _run {
    my ($self, $file)= @_;
    
    my $exe = $self->executable || return;
    my $param_str = $self->arguments." ".$self->_setparams;
    my $command = $exe." $param_str ".$file;
    
    $self->debug("QuickTree command = $command");
    
    open(my $result, "$command |") || $self->throw("QuickTree call ($command) crashed: $?");
    my $treeio = Bio::TreeIO->new(-format => 'nhx', -fh => $result);
    my $tree = $treeio->next_tree;
    close($result);
    
    # if bootstraps were enabled, the bootstraps are the ids; convert to
# bootstrap and no id
if ($self->boot) { my @nodes = $tree->get_nodes; my %non_internal = map { $_ => 1 } ($tree->get_leaf_nodes, $tree->get_root_node); foreach my $node (@nodes) { next if exists $non_internal{$node}; $node->bootstrap && next; # protect ourselves incase the parser improves
$node->bootstrap($node->id); $node->id(''); } } return $tree;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my $self = shift;
    my $param_string = '-in a -out t';
    
    $param_string .= ' -upgma' if $self->upgma;
    $param_string .= ' -kimura' if $self->kimura;
    $param_string .= ' -boot '.$self->boot if $self->boot;
    
    return $param_string;
}
_writeAlignFiledescriptionprevnextTop
sub _writeAlignFile {
    my ($self, $align) = @_;
    
    my ($tfh, $tempfile) = $self->io->tempfile(-dir=>$self->tempdir);
    
    my $out = Bio::AlignIO->new('-fh'     => $tfh, 
				'-format' => 'stockholm');
    $out->write_aln($align);
    $out->close();
    $out = undef;
    close($tfh);
    undef $tfh;
    return $tempfile;
}

1;
}
General documentation
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
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _