TFBS::SiteSet(3pm) User Contributed Perl Documentation TFBS::SiteSet(3pm)NAME
TFBS::SiteSet - a set of TFBS::Site objects
SYNOPSIS
my $site_set = TFBS::SiteSet->new(@list_of_site_objects);
# add a TFBS::Site object to set:
$site_set->add_site($site_obj);
# append another TFBS::SiteSet contents:
$site_pair_set->add_site_set($site_obj);
# create an iterator:
my $it = $site_set->Iterator(-sort_by => 'start');
DESCRIPTION
TFBS::SiteSet is an aggregate class that contains a collection of TFBS::Site objects. It can be created anew and filled with TFBS::Site
object. It is also returned by search_seq() method call of some TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM).
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.
add_site
Title : add_site
Usage : $siteset->add_site($site_object)
$siteset->add_site(@list_of_site_objects)
Function: adds TFBS::Site objects to an existing TFBS::SiteSet object
Returns : $sitepair object (usually ignored)
Args : A list of TFBS::Site objects to add
add_site_set
Title : add_site_set
Usage : $siteset->add_site_set($site_set_object)
$siteset->add_site(@list_of_site_set_objects)
Function: adds the contents of other TFBS::SiteSet objects
to an existing TFBS::SiteSet object
Returns : $siteset object (usually ignored)
Args : A list of TFBS::SiteSet objects whose contents should be
added to $siteset
size
Title : size
Usage : my $size = $siteset->size()
Function: returns a number of TFBS::Site objects contained in the set
Returns : a scalar (integer)
Args : none
Iterator
Title : Iterator
Usage : my $siteset_iterator =
$siteset->Iterator(-sort_by =>'start');
while (my $site = $siteset_iterator->next) {
# do whatever you want with individual matrix objects
}
Function: Returns an iterator object that can be used to go through
all members of the set (TFBS::Site objects)
Returns : an iterator object (currently undocumentened in TFBS -
but understands the 'next' method)
Args : -sort_by # optional - currently it accepts
# (default sort order in parenthetse)
# 'name' (pattern name, alphabetically)
# 'ID' (pattern/matrix ID, alphabetically)
# 'start' (site start in sequence,
# numerically,increasing order)
# 'end' (site end in sequence,
# numerically, increasing order)
# 'score' (numerically, decreasing order)
-reverse # optional - reverses the default sorting order if true
GFF
Title : GFF
Usage : print $siteset->GFF();
: print $siteset->GFF($gff_formatter)
Function: returns a "standard" multiline GFF string
Returns : a string (multiline, newline terminated)
Args : a $gff_formatter function reference (optional)
perl v5.14.2 2008-01-24 TFBS::SiteSet(3pm)
Check Out this Related Man Page
TFBS::Site(3pm) User Contributed Perl Documentation TFBS::Site(3pm)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 acces 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.
perl v5.14.2 2008-01-24 TFBS::Site(3pm)