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.IX Title "Bio::Tools::Run::Phylo::Gumby 3pm"
.TH Bio::Tools::Run::Phylo::Gumby 3pm "2018-09-14" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::Gumby \- Wrapper for gumby
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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) = $feat\->get_tag_values(\*(Aqpvalue\*(Aq);
\&    my ($kind) = $feat\->get_tag_values(\*(Aqkind\*(Aq); # \*(Aqall\*(Aq, \*(Aqexon\*(Aq or \*(Aqnonexon\*(Aq
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
You can try supplying normal gumby command-line arguments to \fInew()\fR, eg.
.PP
.Vb 1
\&  $factory\->new(\-ratio => 2);
.Ve
.PP
or calling arg-named methods (excluding the initial hyphen, eg.
.PP
.Vb 1
\&  $factory\->econs(1);
.Ve
.PP
to set the \-econs arg).
.PP
You will need to enable this Gumby wrapper to find the gumby program.
This can be done in (at least) three ways:
.PP
.Vb 4
\& 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} = \*(Aq/home/username/gumby/\*(Aq }
\&    use Bio::Tools::Run::Phylo::Gumby;
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : None
.Ve
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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
.Ve
.SS "annots"
.IX Subsection "annots"
.Vb 10
\& 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.
.Ve
.SS "run"
.IX Subsection "run"
.Vb 10
\& 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 (\*(AqHomo_sapiens\*(Aq), 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 \*(AqHomo_sapiens\*(Aq sequence had the range 20..60 in your alignment,
\&           the first Gumby result might be 1..5 which is corrected to 20..24.
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 5
\& 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
.Ve