tfbs::patterngen(3pm) [debian man page]

TFBS::PatternGen(3pm)					User Contributed Perl Documentation				     TFBS::PatternGen(3pm)

NAME

       TFBS::PatternGen - a base class for pattern generators

DESCRIPTION

       TFBS::PatternGen is a base classs providing methods common to all pattern generating modules. It is meant to be inherited by a concrete
       pattern generator, which must have its own constructor.

   pattern
	Title	: pattern
	Usage	: my $pattern_obj = $patterngen->pattern()
	Function: retrieves a pattern object produced by the pattern generator
	Returns : a pattern object (currently available pattern generators
		  return a TFBS::Matrix::PFM object)
	Args	: none
	Warning : If a pattern generator produces more than one pattern,
		  this method call returns only the first one and prints
		  a warning on STDERR, In those cases you should use
		  I<all_patterns> or I<patternSet> methods.

   patternSet
	Title	: patternSet
	Usage	: my $patternSet = $patterngen->patternSet()
	Function: retrieves a pattern set object containing all the patterns
		  produced by the pattern generator
	Returns : a pattern set object (currently available pattern generators
		  return a TFBS::MatrixSet object)
	Args	: none

   all_patterns
	Title	: all_patterns
	Usage	: my @patterns = $patterngen->all_patterns()
	Function: retrieves an array of pattern objects
		  produced by the pattern generator
	Returns : an array of pattern set objects (currently available
		  pattern generators return an array of
		  TFBS::Matrix::PFM objects)
	Args	: none

perl v5.14.2							    2008-01-24						     TFBS::PatternGen(3pm)

TFBS::PatternGen::AnnSpec(3pm)				User Contributed Perl Documentation			    TFBS::PatternGen::AnnSpec(3pm)

NAME

       TFBS::PatternGen::AnnSpec - a pattern factory that uses the AnnSpec program (version 2.1)

SYNOPSIS

	   my $patterngen =
		   TFBS::PatternGen::AnnSpec->new(-seq_file=>'sequences.fa',
						   -binary => 'ann-spec '

	   my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object

DESCRIPTION

       TFBS::PatternGen::AnnSpec builds position frequency matrices using an external program AnnSpec (Workman, C. and Stormo, G.D.(2000) ANN-
       Spec: A method for discovering transcription factor binding sites with improved specificity. Proc. Pacific Symposium on Biocomputing 2000).

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Wynand Alkema
       Wynand Alkema <Wynand.Alkema@cgb.ki.se<gt>

   new
	Title	: new
	Usage	: my $pattrengen = TFBS::PatternGen::AnnSpec->new(%args);
	Function: the constructor for the TFBS::PatternGen::AnnSpec object
	Returns : a TFBS::PatternGen::AnnSpec object
	Args	: This method takes named arguments;
		   you must specify one of the following three
		   -seq_list	 # a reference to an array of strings
				 #   and/or Bio::Seq objects
		     # or
		   -seq_stream	 # A Bio::SeqIO object
		     # or
		   -seq_file	 # the name of the fasta file containing
				 #   all the sequences
		  Other arguments are:
		   -binary	 # a fully qualified path to the 'meme' executable
				 #  OPTIONAL: default 'ann-spec'
		   -additional_params  # a string containing additional
				       #   command-line switches for the
				       #   ann-spec program

   pattern
   all_patterns
   patternSet
       The three methods listed above are used for the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
       TFBS::PatternGen for details.

perl v5.14.2							    2008-01-24					    TFBS::PatternGen::AnnSpec(3pm)