Bio::Tools::Run::PhyloUseraContributBio::Tools::Run::Phylo::Phast::PhyloFit(3)NAMEBio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit
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;
FEEDBACK
Mailing Lists
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
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 Bugs
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 Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : None
new
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
run
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
_setparams
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
perl v5.14.120Bio::Tools::Run::Phylo::Phast::PhyloFit(3)
