Bio::Tools::Run::FootPrinter man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

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 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

perl v5.14.1			  2011-07-21   Bio::Tools::Run::FootPrinter(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net