NAME

       TFBS::Site - a nucleotide sequence feature object representing (possibly putative)
       transcription factor binding site.

SYNOPSIS

           # manual creation of site object;
           # for details, see documentation of Bio::SeqFeature::Generic;

           my $site = TFBS::Site
                         (-start => $start_pos,     # integer
                          -end   => $end_pos,       # integer
                          -score => $score,         # float
                          -source => "TFBS",        # string
                          -primary => "TF binding site",  # primary tag
                          -strand => $strand,       # -1, 0 or 1
                          -seqobj => $seqobj,       # a Bio::Seq object whose sequence
                                                    #            contains the site
                          -pattern => $pattern_obj  # usu. TFBS::Matrix:PWM obj.
                          -);

           # Searching sequence with a pattern (PWM) and retrieving individual sites:
           #
           #   The following objects should be defined for this example:
           #       $pwm    -   a TFBS::Matrix::PWM object
           #       $seqobj -   a Bio::Seq object
           #   Consult the documentation for the above modules if you do not know
           #   how to create them.

           #   Scanning sequence with $pwm returns a TFBS::SiteSet object:

           my $site_set = $pwm->search_seq(-seqobj => $seqobj,
                                           -threshold => "80%");

           #   To retrieve individual sites from $site_set, create an iterator obj:

           my $site_iterator = $site_set->Iterator(-sort_by => "score");

           while (my $site = $site_iterator->next())  {
               # do something with $site
           }

DESCRIPTION

       TFBS::Site object holds data for a (possibly predicted) transcription factor binding site
       on a nucleotide sequence (start, end, strand, score, tags, as well as references to the
       corresponding sequence and pattern objects). TFBS::Site is a subclass of
       Bio::SeqFeature::Generic and has access to all of its method. Additionally, it contains
       the pattern() method, an accessor for pattern object associated with the site object.

FEEDBACK

       Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

       Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       preceded with an underscore.

       TFBS::Site is a class that extends Bio::SeqFeature::Generic. Please consult
       Bio::SeqFeature::Generic documentation for other available methods.

   new
        Title   : new
        Usage   : my $site = TFBS::Site->new(%args)
        Function: constructor for the TFBS::Site object
        Returns : TFBS::Site object
        Args    : -start,       # integer
                  -end,         # integer
                  -strand,      # -1, 0 or 1
                  -score,       # float
                  -source,      # string (method used to detect it)
                  -primary,     # string (primary tag)
                  -seqobj,      # a Bio::Seq object
                  -pattern      # a pattern object, usu. TFBS::Matrix::PWM

   pattern
        Title   : pattern
        Usage   : my $pattern = $site->pattern();  # gets the pattern
                  $site->pattern($pwm);            # sets the pattern to $pwm
        Function: gets/sets the pattern object associated with the site
        Returns : pattern object, here TFBS::Matrix::PWM object
        Args    : pattern object (optional, for setting the pattern only)

   rel_score
        Title   : rel_score
        Usage   : my $percent_score = $site->rel_score() * 100;  # gets the pattern
        Function: gets relative score (between 0.0 to 1.0) with respect of the score
                  range of the associated pattern (matrix)
        Returns : floating point number between 0 and 1,
                  or undef if pattern not defined
        Args    : none

   GFF
        Title   : GFF
        Usage   : print $site->GFF();
                : print $site->GFF($gff_formatter)
        Function: returns a "standard" GFF string - the "generic" gff_string
                  method is left untouched for possible customizations
        Returns : a string (NOT newline terminated! )
        Args    : a $gff_formatter function reference (optional)

   location
   start
   end
   length
   score
   frame
   sub_SeqFeature
   add_sub_SeqFeature
   flush_sub_SeqFeature
   primary_tag
   source_tag
   has_tag
   add_tag_value
   each_tag_value
   all_tags
   remove_tag
   attach_seq
   seq
   entire_seq
   seq_id
   annotation
   gff_format
   gff_string
       The above methods are inherited from Bio::SeqFeature::Generic.  Please see
       Bio::SeqFeature::Generic for details on their usage.