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Bio::Tools::Run::MatchUser Contributed Perl DocumentaBio::Tools::Run::Match(3)

NAME
       Bio::Tools::Run::Match - Wrapper for Transfac's match(TM)

SYNOPSIS
	 use Bio::Tools::Run::Match;

	 # Make a Match factory
	 $factory = Bio::Tools::Run::Match->new(-mxlib => '/path/to/matrix.dat');

	 # Run Match on an sequence object
	 my @results = $factory->run($bio_seq);

	 # look at the results
	 foreach my $feat (@results) {
	   my $seq_id = $feat->seq_id;
	   my $start = $feat->start;
	   my $end = $feat->end;
	   my $score = $feat->score;
	   my ($pvalue) = $feat->get_tag_values('pvalue');
	 }

DESCRIPTION
       This is a wrapper for running the match(TM) program supplied with
       Transfac Pro distributions.

       You can try supplying normal match command-line arguments to new(), eg.
       new(-b => 1) or calling arg-named methods (excluding the initial
       hyphens, eg. $factory->b(1) to set the -b option to true).

       Histogram output isn't supported. -p is supported by using -mxprf, see
       the docs of new() for details.

       You will need to enable this match wrapper to find the match
       executable.  This can be done in (at least) three ways:

	1. Make sure match is in your path.
	2. Define an environmental variable MATCHDIR which is a
	   directory which contains the match executable:
	   In bash:

	   export MATCHDIR=/home/username/match/

	   In csh/tcsh:

	   setenv MATCHDIR /home/username/match

	3. Include a definition of an environmental variable MATCHDIR in
	   every script that will use this match wrapper module, e.g.:

	   BEGIN { $ENV{MATCHDIR} = '/home/username/match/' }
	   use Bio::Tools::Run::Match;

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

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

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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	: None

   new
	Title	: new
	Usage	: $factory = Bio::Tools::Run::Match->new()
	Function: creates a new MCS factory
	Returns : Bio::Tools::Run::MCS
	Args	: The following args can either be supplied here or set by calling
		  arg-named methods (eg. $factory->imcut(2) ).

		  -mxlib  => path to the matrix.dat file containing Transfac matricies
		  -mxprf  => path to a profile file | [core_thresh, [matrix_thresh]]
			     (defaults to a standard one based on the mxlib provided if
			     file not supplied, using core_thresh and matrix_thresh
			     values if those are supplied instead)
		  -imcut  => floating point number, the importance cutoff
		  -b | -u => boolean, mutually exclusive

   run
	Title	: run
	Usage	: $result = $factory->run($bio_seqi_object);
	Function: Runs match on a sequence.
	Returns : list of Bio::SeqFeatureI feature objects
	Args	: Bio::SeqI compliant object

		  NB: mxlib has to have been set prior to calling run(), either as an
		  argument to new() or by calling mxlib().

   _setparams
	Title	: _setparams
	Usage	: Internal function, not to be called directly
	Function: Creates a string of params to be used in the command string
	Returns : string of params
	Args	: none

perl v5.14.1			  2011-07-21	     Bio::Tools::Run::Match(3)
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