Class: OligoDesigner

Inherits:
Object
  • Object
show all
Defined in:
lib/oligo_designer.rb

Defined Under Namespace

Classes: Oligo

Instance Method Summary collapse

Instance Method Details

#just_below(nucleotide_string, max_temperature, gc_clamp = 0) ⇒ Object

Given a sequence, find the subsequence that starts at the 5’ end (ie the start of the string), and ends when the melting temperature is maximal but below the max_temperature requires the oligotm program to be available on the cmd line.

  • nucleotide_string: the full sequence that we are choosing oligos from

  • max_temperature: the maximal temperature to start things off at

  • gc_clamp: require this many G or C residues at the 3’ end of the oligo.



10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
 
# File 'lib/oligo_designer.rb', line 10

def just_below(nucleotide_string, max_temperature, gc_clamp=0)
  # initial conditions
  guess = 0
  guess_temp = 0

  # loop around
  while guess_temp < max_temperature
    guess += 1
    guess_temp = melting_temperature nucleotide_string[0..guess-1]

    # break if there's we've reached the end of the line
    return nucleotide_string if guess > nucleotide_string.length
  end
  return nucleotide_string[0..guess-2]
end

#melting_temperature(nucleotide_string) ⇒ Object

A simple method to return the melting temperature of a particular nucleotide string. Uses oligotm on the command line.



78
79
80
81
 
# File 'lib/oligo_designer.rb', line 78

def melting_temperature(nucleotide_string)
  #`oligotm -tp 1 -sc 1 -n 0.8 -d 500 -mv 0 -dv 50 '#{nucleotide_string}'`.to_f
  `oligotm -tp 1 -sc 1 -n 0.2 -d 2 -mv 1 '#{nucleotide_string}'`.to_f
end

#possible_oligos_ordered_by_temperature_difference(nucleotide_string, min_temperature, best_temperature, max_temperature, gc_clamp) ⇒ Object Also known as: order

Rank oligomers within some constraints.



27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
 
# File 'lib/oligo_designer.rb', line 27

def possible_oligos_ordered_by_temperature_difference(nucleotide_string, min_temperature, best_temperature, max_temperature, gc_clamp)
  default_distance = lambda do |seq, tm|
  # fails constraints if not enough GC clamp
    if seq[seq.length-gc_clamp..seq.length-1].gsub(/[gc]/i,'').length > 0
    false
    else
    # the sequence is within contraints. The melting temperature closest to the best wins.
    tm_diff = (best_temperature-tm).abs
    tm_diff
    end
  end

  # initial conditions
  guess = 0
  guess_temp = 0
  # arrays to fill with possible possibles
  oligos = []

  # loop around, until max temperature is reached
  while guess_temp < max_temperature
    guess += 1
    seq = nucleotide_string[0..guess-1]
    guess_temp = melting_temperature seq

    # Add it to the list if there is enough temperature
    if guess_temp > min_temperature and guess_temp < max_temperature
    o = Oligo.new
    o.sequence = seq
    o.tm = guess_temp
    oligos.push o
    end

    # break if there's we've reached the end of the line
    break if guess > nucleotide_string.length-1
  end

  # Convert sequences into distances
  oligos.each do |oligo|
    oligo.distance = default_distance.call(oligo.sequence, oligo.tm)
  end

  # remove sequences that don't meet the constraints, and sort the rest with
  # smallest distance first
  return oligos.reject{|o| o.distance == false}.sort{|a,b|
    a.distance<=>b.distance
  }.collect{|o| o.sequence}
end