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Bio::Tools::Run::FootPUsereContributed Perl DocBio::Tools::Run::FootPrinter(3)

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

perl v5.24.1			  2017-07-08   Bio::Tools::Run::FootPrinter(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shawn Hoon | APPENDIX | Bio::Tools::Run::Wrapper methods

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