Class Bio::Meme::Motif
In: lib/bio/appl/meme/motif.rb
Parent: Object

Description

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

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

Methods

length   new  

Attributes

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

Public Class methods

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

[Source]

    # File lib/bio/appl/meme/motif.rb, line 31
31:     def initialize(sequence_name, strand, motif, start_pos, end_pos, pvalue)
32:       @sequence_name = sequence_name.to_s
33:       @strand = strand.to_s
34:       @motif = motif.to_i
35:       @start_pos = start_pos.to_i
36:       @end_pos = end_pos.to_i
37:       @pvalue = pvalue.to_f
38:     end

Public Instance methods

Computes the motif length

[Source]

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

[Validate]