Module: SSW::AASeq

Defined in:
lib/ssw/aaseq.rb

Constant Summary collapse

AAELEMENTS = 
['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G',
'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S',
'T', 'W', 'Y', 'V', 'B', 'Z', 'X', '*'].freeze
AA2INT = 
{ 'A' => 0,  'a' => 0,
'R' => 1,  'r' => 1,
'N' => 2,  'n' => 2,
'D' => 3,  'd' => 3,
'C' => 4,  'c' => 4,
'Q' => 5,  'q' => 5,
'E' => 6,  'e' => 6,
'G' => 7,  'g' => 7,
'H' => 8,  'h' => 8,
'I' => 9,  'i' => 9,
'L' => 10, 'l' => 10,
'K' => 11, 'k' => 11,
'M' => 12, 'm' => 12,
'F' => 13, 'f' => 13,
'P' => 14, 'p' => 14,
'S' => 15, 's' => 15,
'T' => 16, 't' => 16,
'W' => 17, 'w' => 17,
'Y' => 18, 'y' => 18,
'V' => 19, 'v' => 19,
'B' => 20, 'b' => 20,
'Z' => 21, 'z' => 21,
'X' => 22, 'x' => 22,
'*' => 23 }.freeze
INT2AA = 
{ 0 => 'A', 1 => 'R', 2 => 'N', 3 => 'D',
4 => 'C', 5 => 'Q', 6 => 'E', 7 => 'G',
8 => 'H', 9 => 'I', 10 => 'L', 11 => 'K',
12 => 'M', 13 => 'F', 14 => 'P', 15 => 'S',
16 => 'T', 17 => 'W', 18 => 'Y', 19 => 'V',
20 => 'B', 21 => 'Z', 22 => 'X', 23 => '*' }.freeze

Class Method Summary collapse

Class Method Details

.from_int_array(arr) ⇒ String

Transform numerical sequence into amino acid sequence.

Examples:

SSW::AASeq.from_int_array([0, 1, 2, 3]) #=> "ARND"

Parameters:

  • arr (Array) —

    int array

Returns:

  • (String) —

    amino acid sequence

Raises:

  • (ArgumentError) 


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# File 'lib/ssw/aaseq.rb', line 63

def from_int_array(arr)
  raise ArgumentError, 'arr must be an Array' unless arr.is_a? Array

  arr.map do |i|
    INT2AA[i] || '*'
  end.join
end

.to_int_array(seq) ⇒ Array

Transform amino acid sequence into numerical sequence.

Examples:

SSW::AASeq.to_int_array("ARND") #=> [0, 1, 2, 3]

Parameters:

  • seq (String) —

    amin acid sequence

Returns:

  • (Array) —

    int array

Raises:

  • (ArgumentError) 


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# File 'lib/ssw/aaseq.rb', line 49

def to_int_array(seq)
  raise ArgumentError, 'seq must be a string' unless seq.is_a? String

  seq.each_char.map do |base|
    AA2INT[base] || AA2INT['*']
  end
end