Class: ViralSeq::DRMs

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

Class Method Summary collapse

Class Method Details

.sdrm_hash(options) ⇒ Hash

function to retrieve sdrm positions as a hash

Parameters:

  • ref_option (Symbol) —

    , name of reference genomes, options are ‘:hiv_pr`, `:hiv_rt`, `:hiv_in`, `hcv_ns5a`

Returns:

  • (Hash) —

    Hash of :position_number => [ ‘wildtype_codon’, [‘mutation_codons’]]



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# File 'lib/viral_seq/sdrm.rb', line 8

def sdrm_hash(options)
  sdrm = {}
  case options
  when :hcv_ns5a
    sdrm[28] = ['M',['T']]
    sdrm[30] = ['L',['H','K','R','Q','A','S','D']]
    sdrm[31] = ['L',['M','V','F']]
    sdrm[32] = ['P',['L']]
    sdrm[44] = ['K',['R']]
    sdrm[58] = ['H',['D','P','S']]
    sdrm[64] = ['T',['A','S']]
    sdrm[77] = ['P',['A','S']]
    sdrm[78] = ['R',['K']]
    sdrm[79] = ['T',['A']]
    sdrm[83] = ['T',['M']]
    sdrm[85] = ['S',['N','H','Y']]
    sdrm[92] = ['A',['P','T','K','E']]
    sdrm[93] = ['Y',['C','F','H','N']]
    sdrm[107] = ['K',['T','S']]
    sdrm[121] = ['I',['V']]
    sdrm[135] = ['T',['A']]
  when :nrti
    sdrm[41] = ['M',['L']]
    sdrm[65] = ['K',['R']]
    sdrm[67] = ['D',['N','G','E']]
    sdrm[69] = ['T',['D']]
    sdrm[70] = ['K',['R','E']]
    sdrm[74] = ['L',['V','I']]
    sdrm[75] = ['V',['M','T','A','S']]
    sdrm[77] = ['F',['L']]
    sdrm[115] = ['Y',['F']]
    sdrm[116] = ['F',['Y']]
    sdrm[151] = ['Q',['M']]
    sdrm[184] = ['M',['V','I']]
    sdrm[210] = ['L',['W']]
    sdrm[215] = ["T",["Y","F","I","C","D","V","E"]]
    sdrm[219] = ["K",["Q","E","N","R"]]
  when :nnrti
    sdrm[100] = ['L',['I']]
    sdrm[101] = ['K',['E','P']]
    sdrm[103] = ['K',['N','S']]
    sdrm[106] = ['V',['M','A']]
    sdrm[179] = ['V',['F','D']]
    sdrm[181] = ['Y',['C','I','V']]
    sdrm[188] = ['Y',['L','H','C']]
    sdrm[190] = ['G',['A','S','E']]
    sdrm[225] = ['P',['H']]
    sdrm[230] = ['M',['L']]
  when :hiv_pr
    sdrm[23] = ['L',['I']]
    sdrm[24] = ['L',['I']]
    sdrm[30] = ['D',['N']]
    sdrm[32] = ['V',['I']]
    sdrm[46] = ['M',['I','L']]
    sdrm[47] = ['I',['V','A']]
    sdrm[48] = ['G',['V','M']]
    sdrm[50] = ['I',['V','L']]
    sdrm[53] = ['F',['L']]
    sdrm[54] = ['I',['V','L','M','T','A','S']]
    sdrm[73] = ['G',['S','T','C','A']]
    sdrm[76] = ['L',['V']]
    sdrm[82] = ['V',['A','T','S','F','L','C','M']]
    sdrm[83] = ['N',['D']]
    sdrm[84] = ['I',['V','A','C']]
    sdrm[88] = ['N',['D','S']]
    sdrm[90] = ['L',['M']]
  when :hiv_in
    sdrm[66] = ['T',['A','I','K']]
    sdrm[74] = ['L',['M']]
    sdrm[92] = ['E',['Q']]
    sdrm[95] = ['Q',['K']]
    sdrm[97] = ['T',['A']]
    sdrm[121] = ['F',['Y']]
    sdrm[140] = ['G',['A','S','C']]
    sdrm[143] = ["Y",["C","H","R"]]
    sdrm[147] = ['S',['G']]
    sdrm[148] = ['Q',['H','K','R']]
    sdrm[155] = ['N',['S','H']]
  else raise "Input option `#{options}` for ViralSeq::Sequence.sdrm not supported"
  end
  return sdrm
end

.sdrm_json(options) ⇒ Array

function to export SDRM positions as json object

Returns:

  • (Array) —

    json Array of SDRM positions



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# File 'lib/viral_seq/sdrm.rb', line 95

def sdrm_json(options)
  sdrm = ViralSeq::DRMs.sdrm_hash(options)
  json_array = []
  sdrm.each do |pos, muts|
    mutation = {}
    mutation[:position] = pos
    mutation[:wildtypeCodon] = muts[0]
    mutation[:mutationCodons] = muts[1]
    json_array << mutation
  end
  return json_array
end