Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit


         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);


       This is a wrapper for running the phyloFit application by Adam Siepel. You can get details

       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;


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AUTHOR - Sendu Bala



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns : string
        Args    : None

        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns : string
        Args    : None

        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

        Title   : run
        Usage   : $result = $factory->run($fasta_align_file, $newick_tree_file);
                  $result = $factory->run($align_object, $tree_object);
                  $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 compliant object (eg. a
                  The species tree can be provided as a newick format tree filename
                  or a Bio::Tree::TreeI compliant 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

        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 v5.24.1                                2017-01-1Bio::Tools::Run::Phylo::Phast::PhyloFit(3pm)