Bio::Tools::Run::FootPrinter.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 enviroment 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://bugzilla.open-bio.org/
 
 

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