NAME

       Bio::Tools::Run::Phylo::Gumby - Wrapper for gumby

SYNOPSIS

         use Bio::Tools::Run::Phylo::Gumby;

         # Make a Gumby factory
         $factory = Bio::Tools::Run::Phylo::Gumby->new();

         # Run gumby with an alignment and tree file
         my @results = $factory->run($alignfilename, $treefilename);

         # or with alignment object and tree objects
         @results = $factory->run($bio_simplalign, $bio_tree_tree);

         # or with alignment object and Bio::DB::Taxonomy object
         @results = $factory->run($bio_simplalign, $bio_db_taxonomy);

         # specify the positions of exons in (at least) one of the alignment sequences
         # to get better results
         $factory->econs(1);
         $factory->annots($gff_filename);
         @results = $factory->run($alignfilename, $treefilename);

         # or using feature objects
         $factory->annots(@bio_seqfeature_objects);
         @results = $factory->run($alignfilename, $treefilename);

         # (mixtures of all the above are possible)

         # look at the results
         foreach my $feat (@results) {
           my $seq_id = $feat->seq_id;
           my $start = $feat->start;
           my $end = $feat->end;
           my $score = $feat->score;
           my ($pvalue) = $feat->get_tag_values('pvalue');
           my ($kind) = $feat->get_tag_values('kind'); # 'all', 'exon' or 'nonexon'
         }

DESCRIPTION

       This is a wrapper for running the gumby application by Shyam Prabhakar. You can get
       details here: http://pga.lbl.gov/gumby/. Gumby is used for phylogenetic footprinting/
       shadowing.

       You can try supplying normal gumby command-line arguments to new(), eg.

         $factory->new(-ratio => 2);

       or calling arg-named methods (excluding the initial hyphen, eg.

         $factory->econs(1);

       to set the -econs arg).

       You will need to enable this Gumby wrapper to find the gumby program.  This can be done in
       (at least) three ways:

        1. Make sure the gumby executable is in your path.
        2. Define an environmental variable GUMBYDIR which is a
           directory which contains the gumby application:
           In bash:

           export GUMBYDIR=/home/username/gumby/

           In csh/tcsh:

           setenv GUMBYDIR /home/username/gumby

        3. Include a definition of an environmental variable GUMBYDIR in
           every script that will use this Gumby wrapper module, e.g.:

           BEGIN { $ENV{GUMBYDIR} = '/home/username/gumby/' }
           use Bio::Tools::Run::Phylo::Gumby;

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://redmine.open-bio.org/projects/bioperl/

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::Gumby->new()
        Function: creates a new Gumby factory
        Returns : Bio::Tools::Run::Phylo::Gumby
        Args    : Most options understood by gumby can be supplied as key =>
                  value pairs.

                  These options can NOT be used with this wrapper:
                  o
                  minseq
                  blklen

   annots
        Title   : annots
        Usage   : $factory->annots(@gff_filenames)
        Function: Specify annotation files for gumby to use
        Returns : string of absolute filepaths to gff files
        Args    : list of gff filenames (can be relative), where the first column
                  corresponds to a sequence id from the alignment that will be supplied
                  to run()
                  OR
                  list of Bio::SeqFeatureI objects, which have seq_id() values that
                  will correspond to the sequence ids from the alignment that will
                  be supplied to run() (the objects will be grouped by seq_id and
                  output to gff files for use by gumby; filepaths to those tempfiles
                  will be returned). Note that all features must have source, seq_id
                  and primary_tag set or none will be used.

                  NB: feature coordinates must be relative to the parts of the
                  sequences in the alignment you will supply, as though numbering
                  started at 1 for each each sequence in the alignment. There is
                  currently no automatic correction for this.

   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 gumby on an alignment.
        Returns : list of Bio::SeqFeature::Annotated (one per prediction and sequence)
        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
                  Bio::SimpleAlign).
                  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 have the
                  spaces removed to form the sequence names, eg. Homosapiens.
                  Underscores may also be used for either or both of sequence and node
                  ids ('Homo_sapiens'), but underscores will be removed internally.

                  NB: Gumby treats each sequence in the alignment as starting at
                  position 1. This method returns results with the coordinates
                  corrected so they match the coordinates of your input alignment. Eg.
                  if 'Homo_sapiens' sequence had the range 20..60 in your alignment,
                  the first Gumby result might be 1..5 which is corrected to 20..24.

   _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