Bio::Tools::Run::MCS(3pm)				User Contributed Perl Documentation				 Bio::Tools::Run::MCS(3pm)

NAME

       Bio::Tools::Run::MCS - Wrapper for MCS

SYNOPSIS

	 use Bio::Tools::Run::MCS;

	 # Make a MCS factory
	 $factory = Bio::Tools::Run::MCS->new();

	 # Run MCS on an alignment
	 my @results = $factory->run($alignfilename);

	 # or with alignment object
	 @results = $factory->run($bio_simplalign);

	 # 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) = $feat->get_tag_values('pvalue');
	   my ($kind) = $feat->get_tag_values('kind'); # 'all', 'exon' or 'nonexon'
	 }

DESCRIPTION

       This is a wrapper for running the MCS (binCons) scripts by Elliott H Margulies.	You can get details here:
       http://zoo.nhgri.nih.gov/elliott/mcs_doc/. MCS is used for the prediciton of transcription factor binding sites and other regions of the
       genome conserved amongst different species.

       Note that this wrapper assumes you already have alignments, so only uses MCS for the latter stages (the stages involving align2binomial.pl,
       generate_phyloMAX_score.pl and generate_mcs_beta.pl).

       You can try supplying normal MCS command-line arguments to new(), eg.

	 $factory->new(-percentile => 95)

       or calling arg-named methods (excluding the initial hyphens, eg.

	 $factory->percentile(95)

	to set the --percentile arg).

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

	1. Make sure the MCS scripts are in your path.
	2. Define an environmental variable MCSDIR which is a
	   directory which contains the MCS scripts:
	   In bash:

	   export MCSDIR=/home/username/mcs/

	   In csh/tcsh:

	   setenv MCSDIR /home/username/mcs

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

	   BEGIN { $ENV{MCSDIR} = '/home/username/mcs/' }
	   use Bio::Tools::Run::MCS;

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://redmine.open-bio.org/projects/bioperl/

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::MCS->new()
	Function: creates a new MCS factory
	Returns : Bio::Tools::Run::MCS
	Args	: Many options understood by MCS can be supplied as key =>
		  value pairs.

		  These options can NOT be used with this wrapper:
		  ucsc gtf neutral-only fourd-align align-only ar

   run
	Title	: run
	Usage	: $result = $factory->run($align_file_or_object, Bio::Location::Atomic,
					  [Bio::SeqFeatureI]);
	Function: Runs the MCS scripts on an alignment.
	Returns : list of Bio::SeqFeatureI feature objects (with coordinates corrected
		  according to the supplied offset, if any)
	Args	: The first argument represents an alignment, the optional second
		  argument represents the chromosome, stand and end and the optional
		  third argument represents annotation of the exons in the alignment.

		  The alignment can be provided as a multi-fasta format alignment
		  filename, or a Bio::Align::AlignI compliant object (eg. a
		  Bio::SimpleAlign).

		  The position in the genome can be provided as a Bio::Location::Atomic
		  with start, end and seq_id set.

		  The annnotation can be provided as an array of Bio::SeqFeatureI
		  objects.

   _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 v5.12.3							    2011-06-18						 Bio::Tools::Run::MCS(3pm)