Bio::Tools::Run::Phylo::Phast PhyloFit
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Summary
Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::TreeIO
Cwd
File::Spec
Inherit
Bio::Tools::Run::Phylo::PhyloBase
Synopsis
  use Bio::Tools::Run::Phylo::Phast::PhyloFit;
# Make a PhyloFit factory $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new(); # Generate an init.mod file for use by phastCons my $init_file = $factory->run($alignment, $tree);
Description
This is a wrapper for running the phyloFit application by Adam Siepel. You
can get details here: http://compgen.bscb.cornell.edu/~acs/software.html
Currently the interface is extremely simplified. Only the --tree form of usage
is allowed (not --init-model), which means a tree must be supplied with the
alignment (to run()). You can try supplying normal phyloFit arguments to new(),
or calling arg-named methods (excluding initial hyphens and converting others
to underscores, eg. $factory->gaps_as_bases(1) to set the --gaps-as-bases arg).
WARNING: the API may change in the future to allow for greater flexability and
access to more phyloFit features.
You will need to enable this PhyloFit wrapper to find the phast programs (at
least phyloFit itself).
This can be done in (at least) three ways:
 1. Make sure the phyloFit executable is in your path.
2. Define an environmental variable PHASTDIR which is a
directory which contains the phyloFit application:
In bash:
export PHASTDIR=/home/username/phast/bin In csh/tcsh: setenv PHASTDIR /home/username/phast/bin 3. Include a definition of an environmental variable PHASTDIR in every script that will use this PhyloFit wrapper module, e.g.: BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' } use Bio::Tools::Run::Phylo::Phast::PhyloFit;
Methods
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
runDescriptionCode
_run
No description
Code
_setparamsDescriptionCode
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::Phast::PhyloFit->new()
Function: creates a new PhyloFit factory
Returns : Bio::Tools::Run::Phylo::Phast::PhyloFit
Args : Most options understood by phastCons can be supplied as key =>
value pairs. Options that don't normally take a value
should be given a value of 1. You can type the keys as you would on
the command line (eg. '--gaps-as-bases' => 1) or with only a single
hyphen to start and internal hyphens converted to underscores (eg.
-gaps_as_bases => 1) to avoid having to quote the key.
These options can NOT be used with this wrapper currently: msa_format / i out_root / o tree / t help / h lnl / L init_model / M scale_only / B scale_subtree / S no_freqs / f no_rates / n post_probs / P expected_subs / X expected_total_subs / Z column_probs / U windows / w windows_explicit / v
runcodeprevnextTop
 Title   : run
Usage : $result = $factory->run($fasta_align_file, $newick_tree_file);
-or-
$result = $factory->run($align_object, $tree_object);
-or-
$result = $factory->run($align_object, $db_taxonomy_object);
Function: Runs phyloFit on an alignment.
Returns : filename of init.mod file produced
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
filename, or a Bio::Align::AlignI complient object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
or a Bio::Tree::TreeI complient object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
In all cases, the alignment sequence names must correspond to node ids in the species tree. Multi-word species names should be joined with underscores to form the sequence names, eg. Homo_sapiens
_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 : alignment and tree file names
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);
    
    $self->_set_from_args(\@args, -methods => {(map { $_ => $PARAMS{$_} } keys %PARAMS),
                                               (map { $_ => $SWITCHES{$_} } keys %SWITCHES)},
                                  -create => 1);
    
    return $self;
}
rundescriptionprevnextTop
sub run {
    my ($self, $aln, $tree) = @_;
    
    ($aln && $tree) || $self->throw("alignment and tree must be supplied");
    $self->_alignment($aln);
    $tree = $self->_tree($tree);
    
    $tree->force_binary;
    
    # adjust tree node ids to convert spaces to underscores (eg. if tree
# generated from taxonomy)
foreach my $node ($tree->get_leaf_nodes) { my $id = $node->id; $id =~ s/ /_/g; $node->id($id); } # check node and seq names match
$self->_check_names; return $self->_run;
}
_rundescriptionprevnextTop
sub _run {
    my $self = shift;
    
    my $exe = $self->executable || return;
    
    # cd to a temp dir
my $temp_dir = $self->tempdir; my $cwd = Cwd->cwd(); chdir($temp_dir) || $self->throw("Couldn't change to temp dir '$temp_dir'"); my $aln_file = $self->_write_alignment; my $tree_file = $self->_write_tree; #...phyloFit --tree "(human,(mouse,rat))" --msa-format FASTA --out-root init alignment.fa
my $command = $exe.$self->_setparams($aln_file, $tree_file); $self->debug("phyloFit command = $command\n"); system($command) && $self->throw("phyloFit call ($command) crashed: $?"); # cd back again
chdir($cwd) || $self->throw("Couldn't change back to working directory '$cwd'"); return File::Spec->catfile($temp_dir, 'init.mod');
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self, $aln_file, $tree_file) = @_;
    
    my $param_string = ' --tree '.$tree_file;
    $param_string .= ' --msa-format FASTA';
    $param_string .= ' --out-root init';
    
    # --min-informative defaults to 50, but must not be greater than the number
# of bases in the alignment
my $aln = $self->_alignment; my $length = $aln->length; my $min_informative = $self->min_informative || 50; if ($length < $min_informative) { $self->min_informative($length); } $param_string .= $self->SUPER::_setparams(-params => [keys %PARAMS], -switches => [keys %SWITCHES], -double_dash => 1, -underscore_to_dash => 1); $param_string .= ' '.$aln_file; return $param_string; } 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 _