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Contents
#
# = bio/appl/meme/motif.rb - Class to represent a sequence motif
#
# Copyright:: Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>,
#
# License:: The Ruby License
#
# == Description
#
# This file contains a minimal class to represent meme motifs
#
# == References
#
# * http://meme.sdsc.edu/meme/intro.html
#
module Bio
module Meme
# == Description
#
# This class minimally represents a sequence motif according to the MEME program
#
# TODO: integrate with Bio::Sequence class
# TODO: parse PSSM data
#
class Motif
attr_accessor :sequence_name, :strand, :motif, :start_pos, :end_pos, :pvalue
# Creates a new Bio::Meme::Motif object
# arguments are
def initialize(sequence_name, strand, motif, start_pos, end_pos, pvalue)
@sequence_name = sequence_name.to_s
@strand = strand.to_s
@motif = motif.to_i
@start_pos = start_pos.to_i
@end_pos = end_pos.to_i
@pvalue = pvalue.to_f
end
# Computes the motif length
def length
@end_pos - @start_pos
end
end
end
end
Version data entries
15 entries across 15 versions & 1 rubygems