Bio::Tools::Run::Phylo::Gumby man page on Fedora

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Bio::Tools::Run::PhyloUsermContributed Perl DoBio::Tools::Run::Phylo::Gumby(3)

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://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::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 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 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

perl v5.14.1			  2011-07-21  Bio::Tools::Run::Phylo::Gumby(3)
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