Class: Bio::Meme::Motif

Inherits:
Object show all
Defined in:
lib/bio/appl/meme/motif.rb

Overview

Description

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

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(sequence_name, strand, motif, start_pos, end_pos, pvalue) ⇒ Motif

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



31
32
33
34
35
36
37
38
 
# 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

Instance Attribute Details

#end_pos ⇒ Object

Returns the value of attribute end_pos.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def end_pos
  @end_pos
end

#motif ⇒ Object

Returns the value of attribute motif.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def motif
  @motif
end

#pvalue ⇒ Object

Returns the value of attribute pvalue.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def pvalue
  @pvalue
end

#sequence_name ⇒ Object

Returns the value of attribute sequence_name.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def sequence_name
  @sequence_name
end

#start_pos ⇒ Object

Returns the value of attribute start_pos.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def start_pos
  @start_pos
end

#strand ⇒ Object

Returns the value of attribute strand.



27
28
29
 
# File 'lib/bio/appl/meme/motif.rb', line 27

def strand
  @strand
end

Instance Method Details

#length ⇒ Object

Computes the motif length



41
42
43
 
# File 'lib/bio/appl/meme/motif.rb', line 41

def length
  @end_pos - @start_pos
end