Provided by: libbio-perl-run-perl_1.7.2-4_all bug

NAME

       Bio::Tools::Run::FootPrinter - wrapper for the FootPrinter program

SYNOPSIS

         use Bio::Tools::Run::FootPrinter;

         my @params = (size => 10,
                        max_mutations_per_branch => 4,
                        sequence_type => 'upstream',
                        subregion_size => 30,
                        position_change_cost => 5,
                        triplet_filtering => 1,
                        pair_filtering => 1,
                        post_filtering => 1,
                        inversion_cost => 1,
                        max_mutations => 4,
                        tree => "~/software/FootPrinter2.0/tree_of_life" );

         my $fp = Bio::Tools::Run::FootPrinter->new(@params, -verbose => 1);

         my $sio = Bio::SeqIO->new(-file => "seq.fa", -format => "fasta");

         while (my $seq = $sio->next_seq){
           push @seq, $seq;
         }
         my @fp = $fp->run(@seq);

         foreach my $result(@fp){
           print "***************\n".$result->seq_id."\n";
           foreach my $feat($result->sub_SeqFeature){
             print $feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
           }
         }

DESCRIPTION

       From the FootPrinter manual:

       FootPrinter is a program that performs phylogenetic footprinting.  It takes as input a set
       of unaligned orthologous sequences from various species, together with a phylogenetic tree
       relating these species.  It then searches for short regions of the sequences that are
       highly conserved, according to a parsimony criterion.

       The regions identified are good candidates for regulatory elements.  By default, the
       program searches for regions that are well conserved across all of the input sequences,
       but this can be relaxed to find regions conserved in only a subset of the species

   About Footprinter
       Written by Mathieu Blanchette and Martin Tompa. Available here:

         http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz

   Running Footprinter
       To run FootPrinter, you will need to set the environment variable FOOTPRINTER_DIR to where
       the binary is located (even if the executable is in your path). For example:

         setenv FOOTPRINTER_DIR /usr/local/bin/FootPrinter2.0/

   Available Parameters
         PARAM         VALUES        DESCRIPTION
         ------------------------------------------------------------------------
         tree                      <file>     REQUIRED, Tree in Newick Format
                                              to evaluate parsimony score
                                              REQUIRED unless tree_of_life
                                              exists in FOOTPRINTER_DIR
         sequence_type             upstream   Default upstream
                                   downstream
                                   other
         size                      4-16       Specifies the size of the motifs sought
         max_mutations             0-20       maximum parsimony score allowed for the motifs
         max_mutations_per_branch  0-20       Allows at most a fixed number of mutations per
                                              branch of the tree
         losses                    <file>     files give span constraints so that the motifs
                                              reported are statistically significant
                                              Example files
                                              universal([6-9]|1[0-2])(loose|tight)?.config
                                              come with FootPrinter2.0.
                                              Install these in FOOTPRINTER_DIR and use by
                                              setting "losses" to "somewhat significant",
                                              "significant", or "very significant". Do not
                                              set loss_cost.
         loss_cost                 0-20       a cost associated with losing a motif along some
                                              branch of the tre
         subregion_size            1-infinity penalize motifs whose position in the sequences
                                              varies too much
         position_change_cost      0-20       Cost for changing subregion
         triplet_filtering         1/0        pre-filtering step that removes from consideration
                                              any substring that does not have a sufficiently good
                                              pair of matching substrings in some pair of the other
                                              input sequences
         pair_filtering            1/0        Same as triplet filtering, but looks only for one match
                                              per other sequence
         post_filtering            1/0        when used in conjunction with the triplet filtering
                                              option, this often significantly speeds up the program,
                                              while still garanteeing optimal results
         indel_cost                1-5        insertions and deletions will be allowed in the motifs
                                              sought, at the given cost
         inversion_cost            1-5        This option allows for motifs to undergo inversions,
                                              at the given cost. An inversion reverse-complements
                                              the motif.
         details                   1/0        Shows some of the details about the progress of the
                                              computation
         html                      1/0        produce html output (never deleted)
         ps                        1/0        produce postscript output (never deleted)

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 one of the Bioperl mailing lists. 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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

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

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

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    :

   executable
        Title   : executable
        Usage   : my $exe = $footprinter->executable('FootPrinter');
        Function: Finds the full path to the 'FootPrinter' executable
        Returns : string representing the full path to the exe
        Args    : [optional] name of executable to set path to
                  [optional] boolean flag whether or not warn when exe is not found

   new
        Title   : new
        Usage   : $rm->new($seq)
        Function: creates a new wrapper
        Returns:  Bio::Tools::Run::FootPrinter
        Args    : self

   run
        Title   : run
        Usage   : $fp->run(@seq)
        Function: carry out FootPrinter
        Example :
        Returns : An array of SeqFeatures
        Args    : An array of Bio::PrimarySeqI compliant object
                  At least 2 are needed.

   _run
        Title   : _run
        Usage   : $fp->_run ($filename,$param_string)
        Function: internal function that runs FootPrinter
        Example :
        Returns : an array of features
        Args    : the filename to the input sequence, filename to phylo tree
                  and the parameter string

   _setparams()
        Title   : _setparams
        Usage   : Internal function, not to be called directly
        Function:  Create parameter inputs for FootPrinter program
        Example :
        Returns : parameter string to be passed to FootPrinter
        Args    : name of calling object

   _setinput()
        Title   : _setinput
        Usage   : Internal function, not to be called directly
        Function: writes input sequence to file and return the file name
        Example :
        Returns : string
        Args    : a Bio::PrimarySeqI compliant object

Bio::Tools::Run::Wrapper methods

   no_param_checks
        Title   : no_param_checks
        Usage   : $obj->no_param_checks($newval)
        Function: Boolean flag as to whether or not we should
                  trust the sanity checks for parameter values
        Returns : value of no_param_checks
        Args    : newvalue (optional)

   save_tempfiles
        Title   : save_tempfiles
        Usage   : $obj->save_tempfiles($newval)
        Function:
        Returns : value of save_tempfiles
        Args    : newvalue (optional)

   outfile_name
        Title   : outfile_name
        Usage   : my $outfile = $codeml->outfile_name();
        Function: Get/Set the name of the output file for this run
                  (if you wanted to do something special)
        Returns : string
        Args    : [optional] string to set value to

   tempdir
        Title   : tempdir
        Usage   : my $tmpdir = $self->tempdir();
        Function: Retrieve a temporary directory name (which is created)
        Returns : string which is the name of the temporary directory
        Args    : none

   cleanup
        Title   : cleanup
        Usage   : $codeml->cleanup();
        Function: Will cleanup the tempdir directory
        Returns : none
        Args    : none

   io
        Title   : io
        Usage   : $obj->io($newval)
        Function:  Gets a L<Bio::Root::IO> object
        Returns : L<Bio::Root::IO>
        Args    : none