Bio::Tools::Run::FootPrinter(3)

NAME
Bio::Tools::Run::FootPrinter - Wrapper for 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,
              'program'=>"/usr/users/shawnh/software/FootPrinter2.0/FootPrinter",
              'tree'   =>"/usr/users/shawnh/software/FootPrinter2.0/tree_of_life",
              'verbose'=>1);
  my $fp = Bio::Tools::Run::FootPrinter->new(@params);

  my $sio = Bio::SeqIO->new(-file=>"/usr/users/shawnh/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
Taken from 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

Copyright (c) 1999-2002, by Mathieu Blanchette and Martin Tompa.

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl

**NOTE** To run FootPrinter, you will need to set the enviroment variable FOOTPRINTER_DIR to where the binary is located. 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 doesn't 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://bio.perl.org/MailList.html  - About the mailing lists

  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 email or the web:

  bioperl-bugs@bioperl.org
  http://bio.perl.org/bioperl-bugs/

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, obtiained from ENV variable.
 Returns:  string
 Args    :

  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