class Bio::Meme::Motif

Description

This class minimally represents a sequence motif according to the MEME program

TODO: integrate with Bio::Sequence class TODO: parse PSSM data

Attributes

end_pos[RW]
motif[RW]
pvalue[RW]
sequence_name[RW]
start_pos[RW]
strand[RW]

Public Class Methods

new(sequence_name, strand, motif, start_pos, end_pos, pvalue) click to toggle source

Creates a new Bio::Meme::Motif object arguments are

# File lib/bio/appl/meme/motif.rb, line 31
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

Public Instance Methods

length() click to toggle source

Computes the motif length

# File lib/bio/appl/meme/motif.rb, line 41
def length
  @end_pos - @start_pos
end