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Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm

NAME

Bio::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