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

       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)

   locationstartendlengthscoreframesub_SeqFeatureadd_sub_SeqFeatureflush_sub_SeqFeatureprimary_tagsource_taghas_tagadd_tag_valueeach_tag_valueall_tagsremove_tagattach_seqseqentire_seqseq_idannotationgff_formatgff_string
       The above methods are inherited from Bio::SeqFeature::Generic.  Please see Bio::SeqFeature::Generic for
       details on their usage.

perl v5.40.0                                       2024-10-20                                    TFBS::Site(3pm)

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

       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.

       Please send bug reports and other comments to the author.

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

           # 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
           }