viral_seq 0.3.2 → 1.0.0

data/lib/viral_seq/nt_variation.rb

@@ -1,148 +0,0 @@
-# viral_seq/nt_variation
-
-# contain functions to cacluate shannon's entropy, pairwise diversity, and TN93 distance
-#   ViralSeq::shannons_entropy
-#   ViralSeq::nucleotide_pi
-#   ViralSeq::TN93
-
-# ViralSeq.shannons_entropy(sequences)
-#   # calculate Shannon's entropy, Euler's number as the base of logarithm
-#   # https://en.wikipedia.org/wiki/Entropy_(information_theory)
-#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
-#   # it works on both nt and aa sequences
-#   # return a Hash object for entropy score at each position in the alignment {:position => :entropy, ...}
-#   # position starts at 1.
-# =Usage
-#   # example
-#   sequence_file = 'spec/sample_files/sample_sequence_alignment_for_entropy.fasta'
-#   sequence_hash = ViralSeq.fasta_to_hash(sequence_file)
-#   entropy_hash = ViralSeq.shannons_entropy(sequence_hash)
-#   entropy_hash[3]
-#   => 0.0
-#   entropy_hash[14].round(3)
-#   => 0.639
-#   # This example is the sample input of LANL Entropy-One
-#   # https://www.hiv.lanl.gov/content/sequence/ENTROPY/entropy_one.html?sample_input=1
-
-# ViralSeq.nucleotide_pi(sequences)
-#   # Function to calculate nucleotide diversity π.
-#   # Refer to https://en.wikipedia.org/wiki/Nucleotide_diversity
-#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
-#   # nt sequence only
-#   # return π as a Float object
-# =Usage
-#   # example
-#   sequences = %w{ AAGGCCTT ATGGCCTT AAGGCGTT AAGGCCTT AACGCCTT AAGGCCAT }
-#   ViralSeq.nucleotide_pi(sequences)
-#   => 0.16667
-
-# ViralSeq.tn93(sequences)
-#   # TN93 distance function
-#   # tabulate pairwise comparison of sequence pairs in a sequence alignment
-#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
-#   # nt sequence only
-#   # return pairwise distance table in Hash object {:diff => :freq, ... }
-#   # Note: :diff in different positions (Integer), not percentage.
-# =Usage
-#   sequences = %w{ AAGGCCTT ATGGCCTT AAGGCGTT AAGGCCTT AACGCCTT AAGGCCAT }
-#   ViralSeq.tn93(sequences)
-#   => {0=>1, 1=>8, 2=>6}
-
-module ViralSeq
-  # calculate Shannon's entropy, Euler's number as the base of logarithm
-
-  def self.shannons_entropy(sequences)
-    sequences = if sequences.is_a?(Hash)
-                  sequences.values
-                elsif sequences.is_a?(Array)
-                  sequences
-                else
-                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
-                end
-    entropy_hash = {}
-    seq_l = sequences[0].size
-    (0..(seq_l - 1)).each do |position|
-      element = []
-      sequences.each do |seq|
-        element << seq[position]
-      end
-      entropy = 0
-      element.delete('*')
-      element_size = element.size
-      ViralSeq.count(element).each do |_k,v|
-        p = v/element_size.to_f
-        entropy += (-p * Math.log(p))
-      end
-      entropy_hash[(position + 1)] = entropy
-    end
-    return entropy_hash
-  end
-
-  # nucleotide pairwise diversity
-  def self.nucleotide_pi(sequences)
-    sequences = if sequences.is_a?(Hash)
-                  sequences.values
-                elsif sequences.is_a?(Array)
-                  sequences
-                else
-                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
-                end
-    seq_length = sequences[0].size - 1
-    nt_position_hash = {}
-    (0..seq_length).each do |n|
-      nt_position_hash[n] = []
-      sequences.each do |s|
-        nt_position_hash[n] << s[n]
-      end
-    end
-    diver = 0
-    com = 0
-    nt_position_hash.each do |_p,nt|
-      nt.delete_if {|n| n =~ /[^A|^C|^G|^T]/}
-      next if nt.size == 1
-      nt_count = ViralSeq.count(nt)
-      combination = (nt.size)*(nt.size - 1)/2
-      com += combination
-      a = nt_count["A"]
-      c = nt_count["C"]
-      t = nt_count["T"]
-      g = nt_count["G"]
-      div = a*c + a*t + a*g + c*t + c*g + t*g
-      diver += div
-    end
-    pi = (diver/com.to_f).round(5)
-    return pi
-  end
-
-  # TN93 distance function. Input: sequence Array/Hash, output hash: {diff => counts, ...}
-  def self.tn93(sequences)
-    sequences = if sequences.is_a?(Hash)
-                  sequences.values
-                elsif sequences.is_a?(Array)
-                  sequences
-                else
-                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
-                end
-    diff = []
-    seq_hash = ViralSeq.count(sequences)
-    seq_hash.values.each do |v|
-      comb = v * (v - 1) / 2
-      comb.times {diff << 0}
-    end
-
-    seq_hash.keys.combination(2).to_a.each do |pair|
-      s1 = pair[0]
-      s2 = pair[1]
-      diff_temp = ViralSeq.compare_two_seq(s1,s2)
-      comb = seq_hash[s1] * seq_hash[s2]
-      comb.times {diff << diff_temp}
-    end
-
-    count_diff = ViralSeq.count(diff)
-    out_hash = Hash.new(0)
-    Hash[count_diff.sort_by{|k,_v|k}].each do |k,v|
-      out_hash[k] = v
-    end
-    return out_hash
-  end
-end

data/lib/viral_seq/poisson_cutoff.rb

@@ -1,68 +0,0 @@
-# viral_seq/poisson_cutoff.rb
-# define Poission cut-off for minority variants.
-# (Ref: Zhou, et al. J Virol 2015)
-#   ViralSeq::poisson_minority_cutoff
-
-# ViralSeq.poisson_minority_cutoff(sequences, error_rate, fold_cutoff)
-#   # sequences: input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
-#   # error_rate: the redisual sequencing error rate (default = 0.0001),
-#   # fold_cutoff: a fold cut-off to determine poisson minority cut-off. default = 20. i.e. <5% mutations from randome method error.
-#   # example: cut-off = 2 means that mutations appear at least 2 times are very likely to be a true mutation instead of residual methods errors.
-# =Usage
-#   sequence_file = 'spec/sample_files/sample_sequence_for_poisson.fasta'
-#   sequences = ViralSeq.fasta_to_hash(sequence_file)
-#   ViralSeq.poisson_minority_cutoff(sequences)
-#   => 2
-
-
-module ViralSeq
-
-  def self.poisson_minority_cutoff(sequences, error_rate = 0.0001, fold_cutoff = 20)
-    sequences = if sequences.is_a?(Hash)
-                  sequences.values
-                elsif sequences.is_a?(Array)
-                  sequences
-                else
-                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
-                end
-    if sequences.size == 0
-      return 0
-    else
-      cut_off = 1
-      l = sequences[0].size
-      rate = sequences.size * error_rate
-      count_mut = ViralSeq.variant_for_poisson(sequences)
-      max_count = count_mut.keys.max
-      poisson_hash = ViralSeq.poisson_distribution(rate, max_count)
-
-      poisson_hash.each do |k,v|
-        cal = l * v
-        obs = count_mut[k] ? count_mut[k] : 0
-        if obs >= fold_cutoff * cal
-          cut_off = k
-          break
-        end
-      end
-      return cut_off
-    end
-  end
-
-  # Input sequence array. output Variant distribution for Poisson cut-off
-  def self.variant_for_poisson(seq)
-    seq_size = seq.size
-    l = seq[0].size - 1
-    var = []
-    (0..l).to_a.each do |pos|
-      nt = []
-      seq.each do |s|
-        nt << s[pos]
-      end
-      count_nt = ViralSeq.count(nt)
-      v = seq_size - count_nt.values.max
-      var << v
-    end
-    var_count = count(var)
-    var_count.sort_by{|key,_value|key}.to_h
-  end
-
-end

data/lib/viral_seq/refseq.rb

@@ -1,45 +0,0 @@
-# viral_seq/refseq.rb
-# store constants of reference sequences
-
-# sequence of HIV-1 HXB2 (Genbank accession number K03455)
-# https://www.ncbi.nlm.nih.gov/nuccore/K03455
-
-# sequence of for HIV-1 NL43 (Genbank accession number AF324493)
-# https://www.ncbi.nlm.nih.gov/nuccore/AF324493
-
-# sequence of SIV MAC239 (Genbank accession number M33262)
-# https://www.ncbi.nlm.nih.gov/nucleotide/M33262
-
-# ViralSeq::HXB2
-# ViralSeq::NL43
-# ViralSeq::MAC239
-# ViralSeq::check_ref
-
-module ViralSeq
-  HXB2 = "TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
-
-  NL43 = "TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTCAAGTTAGTACCAGTTGAACCAGAGCAAGTAGAAGAGGCCAAATAAGGAGAGAAGAACAGCTTGTTACACCCTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGTATTAGTGTGGAAGTTTGACAGCCTCCTAGCATTTCGTCACATGGCCCGAGAGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTACATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCAAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCGGTATTAAGCGGGGGAGAATTAGATAAATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAACTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGTGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCCTTAGATAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAGGCACAGCAAGCAGCAGCTGACACAGGAAACAACAGCCAGGTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACACATAATCCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGATTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGGAGCGACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATCCAGCTACCATAATGATACAGAAAGGCAATTTTAGGAACCAAAGAAAGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACAGTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAAGGGTGCCCACACTAATGATGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCATAATAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCAATAGGGAAACTAAATTAGGAAAAGCAGGATATGTAACTGACAGAGGAAGACAAAAAGTTGTCCCCCTAACGGACACAACAAATCAGAAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTGACAGACTCACAATATGCATTGGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAATAGAGCAGTTAATAAAAAAGGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATGGGTTGGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTACCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGCCCAGGAATATGGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCTTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTAATTCCAGCAGAGACAGGGCAAGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAGTACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGTGGGCGGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAATAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATCAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAACACATGGAAAAGATTAGTAAAACACCATATGTATATTTCAAGGAAAGCTAAGGACTGGTTTTATAGACATCACTATGAAAGTACTAATCCAAAAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAAATTAGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGACCTAGCAGACCAACTAATTCATCTGCACTATTTTGATTGTTTTTCAGAATCTGCTATAAGAAATACCATATTAGGACGTATAGTTAGTCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAGTACTTGGCACTAGCAGCATTAATAAAACCAAAACAGATAAAGCCACCTTTGCCTAGTGTTAGGAAACTGACAGAGGACAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCATACAATGAATGGACACTAGAGCTTTTAGAGGAACTTAAGAGTGAAGCTGTTAGACATTTTCCTAGGATATGGCTCCATAACTTAGGACAACATATCTATGAAACTTACGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATGACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAGTATCAGCACTTGTGGAGATGGGGGTGGAAATGGGGCACCATGCTCCTTGGGATATTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGATAAGGTGCAGAAAGAATATGCATTCTTTTATAAACTTGATATAGTACCAATAGATAATACCAGCTATAGGTTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGATGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATCCGTATCCAGAGGGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATGCCACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACACTCCCATGCAGAATAAAACAATTTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACTGGGCTGCTATTAACAAGAGATGGTGGTAATAACAACAATGGGTCCGAGATCTTCAGACCTGGAGGAGGCGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCTGCACGTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGATATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAACAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATAACATGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAATCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTAGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAACTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAGCAGCTTATAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTGCTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCAGTATCTCGAGACCTAGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTAACAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCTGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
-
-  MAC239 = "GCATGCACATTTTAAAGGCTTTTGCTAAATATAGCCAAAAGTCCTTCTACAAATTTTCTAAGAGTTCTGATTCAAAGCAGTAACAGGCCTTGTCTCATCATGAACTTTGGCATTTCATCTACAGCTAAGTTTATATCATAAATAGTTCTTTACAGGCAGCACCAACTTATACCCTTATAGCATACTTTACTGTGTGAAAATTGCATCTTTCATTAAGCTTACTGTAAATTTACTGGCTGTCTTCCTTGCAGGTTTCTGGAAGGGATTTATTACAGTGCAAGAAGACATAGAATCTTAGACATATACTTAGAAAAGGAAGAAGGCATCATACCAGATTGGCAGGATTACACCTCAGGACCAGGAATTAGATACCCAAAGACATTTGGCTGGCTATGGAAATTAGTCCCTGTAAATGTATCAGATGAGGCACAGGAGGATGAGGAGCATTATTTAATGCATCCAGCTCAAACTTCCCAGTGGGATGACCCTTGGGGAGAGGTTCTAGCATGGAAGTTTGATCCAACTCTGGCCTACACTTATGAGGCATATGTTAGATACCCAGAAGAGTTTGGAAGCAAGTCAGGCCTGTCAGAGGAAGAGGTTAGAAGAAGGCTAACCGCAAGAGGCCTTCTTAACATGGCTGACAAGAAGGAAACTCGCTGAAACAGCAGGGACTTTCCACAAGGGGATGTTACGGGGAGGTACTGGGGAGGAGCCGGTCGGGAACGCCCACTTTCTTGATGTATAAATATCACTGCATTTCGCTCTGTATTCAGTCGCTCTGCGGAGAGGCTGGCAGATTGAGCCCTGGGAGGTTCTCTCCAGCACTAGCAGGTAGAGCCTGGGTGTTCCCTGCTAGACTCTCACCAGCACTTGGCCGGTGCTGGGCAGAGTGACTCCACGCTTGCTTGCTTAAAGCCCTCTTCAATAAAGCTGCCATTTTAGAAGTAAGCTAGTGTGTGTTCCCATCTCTCCTAGCCGCCGCCTGGTCAACTCGGTACTCAATAATAAGAAGACCCTGGTCTGTTAGGACCCTTTCTGCTTTGGGAAACCGAAGCAGGAAAATCCCTAGCAGATTGGCGCCTGAACAGGGACTTGAAGGAGAGTGAGAGACTCCTGAGTACGGCTGAGTGAAGGCAGTAAGGGCGGCAGGAACCAACCACGACGGAGTGCTCCTATAAAGGCGCGGGTCGGTACCAGACGGCGTGAGGAGCGGGAGAGGAAGAGGCCTCCGGTTGCAGGTAAGTGCAACACAAAAAAGAAATAGCTGTCTTTTATCCAGGAAGGGGTAATAAGATAGAGTGGGAGATGGGCGTGAGAAACTCCGTCTTGTCAGGGAAGAAAGCAGATGAATTAGAAAAAATTAGGCTACGACCCAACGGAAAGAAAAAGTACATGTTGAAGCATGTAGTATGGGCAGCAAATGAATTAGATAGATTTGGATTAGCAGAAAGCCTGTTGGAGAACAAAGAAGGATGTCAAAAAATACTTTCGGTCTTAGCTCCATTAGTGCCAACAGGCTCAGAAAATTTAAAAAGCCTTTATAATACTGTCTGCGTCATCTGGTGCATTCACGCAGAAGAGAAAGTGAAACACACTGAGGAAGCAAAACAGATAGTGCAGAGACACCTAGTGGTGGAAACAGGAACAACAGAAACTATGCCAAAAACAAGTAGACCAACAGCACCATCTAGCGGCAGAGGAGGAAATTACCCAGTACAACAAATAGGTGGTAACTATGTCCACCTGCCATTAAGCCCGAGAACATTAAATGCCTGGGTAAAATTGATAGAGGAAAAGAAATTTGGAGCAGAAGTAGTGCCAGGATTTCAGGCACTGTCAGAAGGTTGCACCCCCTATGACATTAATCAGATGTTAAATTGTGTGGGAGACCATCAAGCGGCTATGCAGATTATCAGAGATATTATAAACGAGGAGGCTGCAGATTGGGACTTGCAGCACCCACAACCAGCTCCACAACAAGGACAACTTAGGGAGCCGTCAGGATCAGATATTGCAGGAACAACTAGTTCAGTAGATGAACAAATCCAGTGGATGTACAGACAACAGAACCCCATACCAGTAGGCAACATTTACAGGAGATGGATCCAACTGGGGTTGCAAAAATGTGTCAGAATGTATAACCCAACAAACATTCTAGATGTAAAACAAGGGCCAAAAGAGCCATTTCAGAGCTATGTAGACAGGTTCTACAAAAGTTTAAGAGCAGAACAGACAGATGCAGCAGTAAAGAATTGGATGACTCAAACACTGCTGATTCAAAATGCTAACCCAGATTGCAAGCTAGTGCTGAAGGGGCTGGGTGTGAATCCCACCCTAGAAGAAATGCTGACGGCTTGTCAAGGAGTAGGGGGGCCGGGACAGAAGGCTAGATTAATGGCAGAAGCCCTGAAAGAGGCCCTCGCACCAGTGCCAATCCCTTTTGCAGCAGCCCAACAGAGGGGACCAAGAAAGCCAATTAAGTGTTGGAATTGTGGGAAAGAGGGACACTCTGCAAGGCAATGCAGAGCCCCAAGAAGACAGGGATGCTGGAAATGTGGAAAAATGGACCATGTTATGGCCAAATGCCCAGACAGACAGGCGGGTTTTTTAGGCCTTGGTCCATGGGGAAAGAAGCCCCGCAATTTCCCCATGGCTCAAGTGCATCAGGGGCTGATGCCAACTGCTCCCCCAGAGGACCCAGCTGTGGATCTGCTAAAGAACTACATGCAGTTGGGCAAGCAGCAGAGAGAAAAGCAGAGAGAAAGCAGAGAGAAGCCTTACAAGGAGGTGACAGAGGATTTGCTGCACCTCAATTCTCTCTTTGGAGGAGACCAGTAGTCACTGCTCATATTGAAGGACAGCCTGTAGAAGTATTACTGGATACAGGGGCTGATGATTCTATTGTAACAGGAATAGAGTTAGGTCCACATTATACCCCAAAAATAGTAGGAGGAATAGGAGGTTTTATTAATACTAAAGAATACAAAAATGTAGAAATAGAAGTTTTAGGCAAAAGGATTAAAGGGACAATCATGACAGGGGACACCCCGATTAACATTTTTGGTAGAAATTTGCTAACAGCTCTGGGGATGTCTCTAAATTTTCCCATAGCTAAAGTAGAGCCTGTAAAAGTCGCCTTAAAGCCAGGAAAGGATGGACCAAAATTGAAGCAGTGGCCATTATCAAAAGAAAAGATAGTTGCATTAAGAGAAATCTGTGAAAAGATGGAAAAGGATGGTCAGTTGGAGGAAGCTCCCCCGACCAATCCATACAACACCCCCACATTTGCTATAAAGAAAAAGGATAAGAACAAATGGAGAATGCTGATAGATTTTAGGGAACTAAATAGGGTCACTCAGGACTTTACGGAAGTCCAATTAGGAATACCACACCCTGCAGGACTAGCAAAAAGGAAAAGAATTACAGTACTGGATATAGGTGATGCATATTTCTCCATACCTCTAGATGAAGAATTTAGGCAGTACACTGCCTTTACTTTACCATCAGTAAATAATGCAGAGCCAGGAAAACGATACATTTATAAGGTTCTGCCTCAGGGATGGAAGGGGTCACCAGCCATCTTCCAATACACTATGAGACATGTGCTAGAACCCTTCAGGAAGGCAAATCCAGATGTGACCTTAGTCCAGTATATGGATGACATCTTAATAGCTAGTGACAGGACAGACCTGGAACATGACAGGGTAGTTTTACAGTCAAAGGAACTCTTGAATAGCATAGGGTTTTCTACCCCAGAAGAGAAATTCCAAAAAGATCCCCCATTTCAATGGATGGGGTACGAATTGTGGCCAACAAAATGGAAGTTGCAAAAGATAGAGTTGCCACAAAGAGAGACCTGGACAGTGAATGATATACAGAAGTTAGTAGGAGTATTAAATTGGGCAGCTCAAATTTATCCAGGTATAAAAACCAAACATCTCTGTAGGTTAATTAGAGGAAAAATGACTCTAACAGAGGAAGTTCAGTGGACTGAGATGGCAGAAGCAGAATATGAGGAAAATAAAATAATTCTCAGTCAGGAACAAGAAGGATGTTATTACCAAGAAGGCAAGCCATTAGAAGCCACGGTAATAAAGAGTCAGGACAATCAGTGGTCTTATAAAATTCACCAAGAAGACAAAATACTGAAAGTAGGAAAATTTGCAAAGATAAAGAATACACATACCAATGGAGTGAGACTATTAGCACATGTAATACAGAAAATAGGAAAGGAAGCAATAGTGATCTGGGGACAGGTCCCAAAATTCCACTTACCAGTTGAGAAGGATGTATGGGAACAGTGGTGGACAGACTATTGGCAGGTAACCTGGATACCGGAATGGGATTTTATCTCAACACCACCGCTAGTAAGATTAGTCTTCAATCTAGTGAAGGACCCTATAGAGGGAGAAGAAACCTATTATACAGATGGATCATGTAATAAACAGTCAAAAGAAGGGAAAGCAGGATATATCACAGATAGGGGCAAAGACAAAGTAAAAGTGTTAGAACAGACTACTAATCAACAAGCAGAATTGGAAGCATTTCTCATGGCATTGACAGACTCAGGGCCAAAGGCAAATATTATAGTAGATTCACAATATGTTATGGGAATAATAACAGGATGCCCTACAGAATCAGAGAGCAGGCTAGTTAATCAAATAATAGAAGAAATGATTAAAAAGTCAGAAATTTATGTAGCATGGGTACCAGCACACAAAGGTATAGGAGGAAACCAAGAAATAGACCACCTAGTTAGTCAAGGGATTAGACAAGTTCTCTTCTTGGAAAAGATAGAGCCAGCACAAGAAGAACATGATAAATACCATAGTAATGTAAAAGAATTGGTATTCAAATTTGGATTACCCAGAATAGTGGCCAGACAGATAGTAGACACCTGTGATAAATGTCATCAGAAAGGAGAGGCTATACATGGGCAGGCAAATTCAGATCTAGGGACTTGGCAAATGGATTGTACCCATCTAGAGGGAAAAATAATCATAGTTGCAGTACATGTAGCTAGTGGATTCATAGAAGCAGAGGTAATTCCACAAGAGACAGGAAGACAGACAGCACTATTTCTGTTAAAATTGGCAGGCAGATGGCCTATTACACATCTACACACAGATAATGGTGCTAACTTTGCTTCGCAAGAAGTAAAGATGGTTGCATGGTGGGCAGGGATAGAGCACACCTTTGGGGTACCATACAATCCACAGAGTCAGGGAGTAGTGGAAGCAATGAATCACCACCTGAAAAATCAAATAGATAGAATCAGGGAACAAGCAAATTCAGTAGAAACCATAGTATTAATGGCAGTTCATTGCATGAATTTTAAAAGAAGGGGAGGAATAGGGGATATGACTCCAGCAGAAAGATTAATTAACATGATCACTACAGAACAAGAGATACAATTTCAACAATCAAAAAACTCAAAATTTAAAAATTTTCGGGTCTATTACAGAGAAGGCAGAGATCAACTGTGGAAGGGACCCGGTGAGCTATTGTGGAAAGGGGAAGGAGCAGTCATCTTAAAGGTAGGGACAGACATTAAGGTAGTACCCAGAAGAAAGGCTAAAATTATCAAAGATTATGGAGGAGGAAAAGAGGTGGATAGCAGTTCCCACATGGAGGATACCGGAGAGGCTAGAGAGGTGGCATAGCCTCATAAAATATCTGAAATATAAAACTAAAGATCTACAAAAGGTTTGCTATGTGCCCCATTTTAAGGTCGGATGGGCATGGTGGACCTGCAGCAGAGTAATCTTCCCACTACAGGAAGGAAGCCATTTAGAAGTACAAGGGTATTGGCATTTGACACCAGAAAAAGGGTGGCTCAGTACTTATGCAGTGAGGATAACCTGGTACTCAAAGAACTTTTGGACAGATGTAACACCAAACTATGCAGACATTTTACTGCATAGCACTTATTTCCCTTGCTTTACAGCGGGAGAAGTGAGAAGGGCCATCAGGGGAGAACAACTGCTGTCTTGCTGCAGGTTCCCGAGAGCTCATAAGTACCAGGTACCAAGCCTACAGTACTTAGCACTGAAAGTAGTAAGCGATGTCAGATCCCAGGGAGAGAATCCCACCTGGAAACAGTGGAGAAGAGACAATAGGAGAGGCCTTCGAATGGCTAAACAGAACAGTAGAGGAGATAAACAGAGAGGCGGTAAACCACCTACCAAGGGAGCTAATTTTCCAGGTTTGGCAAAGGTCTTGGGAATACTGGCATGATGAACAAGGGATGTCACCAAGCTATGTAAAATACAGATACTTGTGTTTAATACAAAAGGCTTTATTTATGCATTGCAAGAAAGGCTGTAGATGTCTAGGGGAAGGACATGGGGCAGGGGGATGGAGACCAGGACCTCCTCCTCCTCCCCCTCCAGGACTAGCATAAATGGAAGAAAGACCTCCAGAAAATGAAGGACCACAAAGGGAACCATGGGATGAATGGGTAGTGGAGGTTCTGGAAGAACTGAAAGAAGAAGCTTTAAAACATTTTGATCCTCGCTTGCTAACTGCACTTGGTAATCATATCTATAATAGACATGGAGACACCCTTGAGGGAGCAGGAGAACTCATTAGAATCCTCCAACGAGCGCTCTTCATGCATTTCAGAGGCGGATGCATCCACTCCAGAATCGGCCAACCTGGGGGAGGAAATCCTCTCTCAGCTATACCGCCCTCTAGAAGCATGCTATAACACATGCTATTGTAAAAAGTGTTGCTACCATTGCCAGTTTTGTTTTCTTAAAAAAGGCTTGGGGATATGTTATGAGCAATCACGAAAGAGAAGAAGAACTCCGAAAAAGGCTAAGGCTAATACATCTTCTGCATCAAACAAGTAAGTATGGGATGTCTTGGGAATCAGCTGCTTATCGCCATCTTGCTTTTAAGTGTCTATGGGATCTATTGTACTCTATATGTCACAGTCTTTTATGGTGTACCAGCTTGGAGGAATGCGACAATTCCCCTCTTTTGTGCAACCAAGAATAGGGATACTTGGGGAACAACTCAGTGCCTACCAGATAATGGTGATTATTCAGAAGTGGCCCTTAATGTTACAGAAAGCTTTGATGCCTGGAATAATACAGTCACAGAACAGGCAATAGAGGATGTATGGCAACTCTTTGAGACCTCAATAAAGCCTTGTGTAAAATTATCCCCATTATGCATTACTATGAGATGCAATAAAAGTGAGACAGATAGATGGGGATTGACAAAATCAATAACAACAACAGCATCAACAACATCAACGACAGCATCAGCAAAAGTAGACATGGTCAATGAGACTAGTTCTTGTATAGCCCAGGATAATTGCACAGGCTTGGAACAAGAGCAAATGATAAGCTGTAAATTCAACATGACAGGGTTAAAAAGAGACAAGAAAAAAGAGTACAATGAAACTTGGTACTCTGCAGATTTGGTATGTGAACAAGGGAATAACACTGGTAATGAAAGTAGATGTTACATGAACCACTGTAACACTTCTGTTATCCAAGAGTCTTGTGACAAACATTATTGGGATGCTATTAGATTTAGGTATTGTGCACCTCCAGGTTATGCTTTGCTTAGATGTAATGACACAAATTATTCAGGCTTTATGCCTAAATGTTCTAAGGTGGTGGTCTCTTCATGCACAAGGATGATGGAGACACAGACTTCTACTTGGTTTGGCTTTAATGGAACTAGAGCAGAAAATAGAACTTATATTTACTGGCATGGTAGGGATAATAGGACTATAATTAGTTTAAATAAGTATTATAATCTAACAATGAAATGTAGAAGACCAGGAAATAAGACAGTTTTACCAGTCACCATTATGTCTGGATTGGTTTTCCACTCACAACCAATCAATGATAGGCCAAAGCAGGCATGGTGTTGGTTTGGAGGAAAATGGAAGGATGCAATAAAAGAGGTGAAGCAGACCATTGTCAAACATCCCAGGTATACTGGAACTAACAATACTGATAAAATCAATTTGACGGCTCCTGGAGGAGGAGATCCGGAAGTTACCTTCATGTGGACAAATTGCAGAGGAGAGTTCCTCTACTGTAAAATGAATTGGTTTCTAAATTGGGTAGAAGATAGGAATACAGCTAACCAGAAGCCAAAGGAACAGCATAAAAGGAATTACGTGCCATGTCATATTAGACAAATAATCAACACTTGGCATAAAGTAGGCAAAAATGTTTATTTGCCTCCAAGAGAGGGAGACCTCACGTGTAACTCCACAGTGACCAGTCTCATAGCAAACATAGATTGGATTGATGGAAACCAAACTAATATCACCATGAGTGCAGAGGTGGCAGAACTGTATCGATTGGAATTGGGAGATTATAAATTAGTAGAGATCACTCCAATTGGCTTGGCCCCCACAGATGTGAAGAGGTACACTACTGGTGGCACCTCAAGAAATAAAAGAGGGGTCTTTGTGCTAGGGTTCTTGGGTTTTCTCGCAACGGCAGGTTCTGCAATGGGCGCGGCGTCGTTGACGCTGACCGCTCAGTCCCGAACTTTATTGGCTGGGATAGTGCAGCAACAGCAACAGCTGTTGGACGTGGTCAAGAGACAACAAGAATTGTTGCGACTGACCGTCTGGGGAACAAAGAACCTCCAGACTAGGGTCACTGCCATCGAGAAGTACTTAAAGGACCAGGCGCAGCTGAATGCTTGGGGATGTGCGTTTAGACAAGTCTGCCACACTACTGTACCATGGCCAAATGCAAGTCTAACACCAAAGTGGAACAATGAGACTTGGCAAGAGTGGGAGCGAAAGGTTGACTTCTTGGAAGAAAATATAACAGCCCTCCTAGAGGAGGCACAAATTCAACAAGAGAAGAACATGTATGAATTACAAAAGTTGAATAGCTGGGATGTGTTTGGCAATTGGTTTGACCTTGCTTCTTGGATAAAGTATATACAATATGGAGTTTATATAGTTGTAGGAGTAATACTGTTAAGAATAGTGATCTATATAGTACAAATGCTAGCTAAGTTAAGGCAGGGGTATAGGCCAGTGTTCTCTTCCCCACCCTCTTATTTCCAGCAGACCCATATCCAACAGGACCCGGCACTGCCAACCAGAGAAGGCAAAGAAAGAGACGGTGGAGAAGGCGGTGGCAACAGCTCCTGGCCTTGGCAGATAGAATATATTCATTTCCTGATCCGCCAACTGATACGCCTCTTGACTTGGCTATTCAGCAACTGCAGAACCTTGCTATCGAGAGTATACCAGATCCTCCAACCAATACTCCAGAGGCTCTCTGCGACCCTACAGAGGATTCGAGAAGTCCTCAGGACTGAACTGACCTACCTACAATATGGGTGGAGCTATTTCCATGAGGCGGTCCAGGCCGTCTGGAGATCTGCGACAGAGACTCTTGCGGGCGCGTGGGGAGACTTATGGGAGACTCTTAGGAGAGGTGGAAGATGGATACTCGCAATCCCCAGGAGGATTAGACAAGGGCTTGAGCTCACTCTCTTGTGAGGGACAGAAATACAATCAGGGACAGTATATGAATACTCCATGGAGAAACCCAGCTGAAGAGAGAGAAAAATTAGCATACAGAAAACAAAATATGGATGATATAGATGAGTAAGATGATGACTTGGTAGGGGTATCAGTGAGGCCAAAAGTTCCCCTAAGAACAATGAGTTACAAATTGGCAATAGACATGTCTCATTTTATAAAAGAAAAGGGGGGACTGGAAGGGATTTATTACAGTGCAAGAAGACATAGAATCTTAGACATATACTTAGAAAAGGAAGAAGGCATCATACCAGATTGGCAGGATTACACCTCAGGACCAGGAATTAGATACCCAAAGACATTTGGCTGGCTATGGAAATTAGTCCCTGTAAATGTATCAGATGAGGCACAGGAGGATGAGGAGCATTATTTAATGCATCCAGCTCAAACTTCCCAGTGGGATGACCCTTGGGGAGAGGTTCTAGCATGGAAGTTTGATCCAACTCTGGCCTACACTTATGAGGCATATGTTAGATACCCAGAAGAGTTTGGAAGCAAGTCAGGCCTGTCAGAGGAAGAGGTTAGAAGAAGGCTAACCGCAAGAGGCCTTCTTAACATGGCTGACAAGAAGGAAACTCGCTGAAACAGCAGGGACTTTCCACAAGGGGATGTTACGGGGAGGTACTGGGGAGGAGCCGGTCGGGAACGCCCACTTTCTTGATGTATAAATATCACTGCATTTCGCTCTGTATTCAGTCGCTCTGCGGAGAGGCTGGCAGATTGAGCCCTGGGAGGTTCTCTCCAGCACTAGCAGGTAGAGCCTGGGTGTTCCCTGCTAGACTCTCACCAGCACTTGGCCGGTGCTGGGCAGAGTGACTCCACGCTTGCTTGCTTAAAGCCCTCTTCAATAAAGCTGCCATTTTAGAAGTAAGCTAGTGTGTGTTCCCATCTCTCCTAGCCGCCGCCTGGTCAACTCGGTACTCAATAATAAGAAGACCCTGGTCTGTTAGGACCCTTTCTGCTTTGGGAAACCGAAGCAGGAAAATCCCTAGCA"
-
-
-  # check if reference option is correct, return chosen 'ref_option'
-  def self.check_ref(ref_option)
-    begin
-      case ref_option
-      when :HXB2
-        HXB2.dup
-      when :NL43
-        NL43.dup
-      when :MAC239
-        MAC239.dup
-      else
-        raise StandardError.new("reference sequence not recognized, choose from 'HXB2' (default), 'NL43', or 'MAC239'.")
-      end
-    rescue StandardError => e
-      puts e.message
-      return nil
-    end
-  end
-
-end

data/lib/viral_seq/sdrm_core.rb

@@ -1,652 +0,0 @@
-# viral_seq/sdrm_core.rb
-# core functions for HIV SDRM analysis using MPID-DR protocol.
-# More details for HIV Surveillance Drug Resistance Mutation (SDRM) can be found at
-# https://hivdb.stanford.edu/pages/surveillance.html
-
-# Including methods as:
-#   ViralSeq::sdrm_nrti
-#   ViralSeq::sdrm_nnrti
-#   ViralSeq::hiv_protease
-#   ViralSeq::sdrm_int
-#   ViralSeq::sdrm_pr_bulk
-#   ViralSeq::sdrm_rt_bulk
-#   ViralSeq::sdrm_in_bulk
-
-# ViralSeq.sdrm_nrti(aa_arry, start_aa)
-# ViralSeq.sdrm_nnrti(aa_arry, start_aa)
-# ViralSeq.hiv_protease(aa_arry, start_aa)
-# ViralSeq.sdrm_int(aa_arry, start_aa)
-#   # funtions to identify SDRMs from a given sequence in an Array object
-#   # function names indicate which HIV drug resistance mutations it can identify
-#   # input an Array object for amino acid sequence ['A', 'M', 'L', ...]
-#   # start_aa is an Integer to indicate codon number of the 1st amino acid sequence in the input aa_array
-#   # return a Hash object for SDRMs identified. {:posiiton =>[:wildtype_codon, :mutation_codon]}
-
-# ViralSeq.sdrm_pr_bulk(sequence_hash, minority_cut_off)
-# ViralSeq.sdrm_rt_bulk(sequence_hash, minority_cut_off)
-# ViralSeq.sdrm_in_bulk(sequence_hash, minority_cut_off)
-#   # functions to identify SDRMs from a sequence hash object.
-#   # name of the functions indicate which region it works on
-#   # works for MPID-DR protocol (dx.doi.org/10.17504/protocols.io.useewbe)
-#   # PR codon 1-99
-#   # RT codon 34-122, 152-236, two regions are linked
-#   # IN codon 53-174
-#   # sequence_hash is a Hash object of sequences {:name => :sequence, ...}
-#   # sequences usually need to be QCed (remove sequences with stop codon and a3g hypermutations) first
-#   # minority_cut_off is the Integer cut-off for minimal abundance of a mutation to be called as valid mutation
-#   # minority_cut_off can be obtained using ViralSeq::poisson_minority_cutoff function
-#   # return [point_mutation_list, linkage_list, report_list]
-# =USAGE
-#   # example (example files from ID:VS053118-0566)
-#   sequence = ViralSeq.fasta_to_hash('spec/sample_files/sample_dr_sequences/pr.fasta')
-#   p_cut_off = ViralSeq.poisson_minority_cutoff(sequences)
-#   pr_sdrm = ViralSeq.sdrm_pr_bulk(sequence, p_cut_off)
-#   puts "region,tcs_number,position,wildtype,mutation,count,%,CI_low,CI_high,label"
-#   pr_sdrm[0].each {|n| puts n.join(',')}
-#   => region,tcs_number,position,wildtype,mutation,count,%,CI_low,CI_high,label
-#   => PR,396,30,D,N,247,0.62374,0.57398,0.67163,
-#   => PR,396,50,I,V,1,0.00253,6.0e-05,0.01399,*
-#   => PR,396,88,N,D,246,0.62121,0.57141,0.66919,
-#
-#   puts "region,tcs_number,linkage,count,%,CI_low,CI_high,label"
-#   pr_sdrm[1].each {|n| puts n.join(',')}
-#   => region,tcs_number,linkage,count,%,CI_low,CI_high,label
-#   => PR,396,D30N+N88D,245,0.61869,0.56884,0.66674,
-#   => PR,396,WT,149,0.37626,0.32837,0.42602,
-#   => PR,396,D30N,1,0.00253,6.0e-05,0.01399,*
-#   => PR,396,D30N+I50V+N88D,1,0.00253,6.0e-05,0.01399,*
-#
-#   puts "position,codon,tcs_number," + ViralSeq::AMINO_ACID_LIST.join(",")
-#   pr_sdrm[2].each {|n|puts n.join(",")}
-#   => position,codon,tcs_number,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*
-#   => PR,1,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,2,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,3,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,4,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,5,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,6,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0
-#   => PR,7,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,8,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,9,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,10,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,11,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0
-#   => PR,12,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,37.8788,62.1212,0.0,0.0,0.0,0.0
-#   => PR,13,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,38.1313,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,61.8687,0.0,0.0,0.0
-#   => PR,14,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,15,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.3737,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,37.6263,0.0,0.0,0.0
-#   => PR,16,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,17,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,18,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.4949,0.5051,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,19,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,20,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,21,396,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,22,396,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,23,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,24,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,25,396,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,26,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,27,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,28,396,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,29,396,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,30,396,0.0,0.0,37.6263,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.3737,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,31,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,32,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0
-#   => PR,33,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.0
-#   => PR,34,396,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,35,396,0.0,0.0,62.1212,37.6263,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,36,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.0
-#   => PR,37,396,0.0,0.0,37.8788,61.8687,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,38,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,39,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.4949,0.0,0.0,0.5051,0.0,0.0,0.0,0.0,0.0
-#   => PR,40,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,41,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,37.8788,0.0,0.0,0.0,0.0,0.0,62.1212,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,42,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0
-#   => PR,43,396,0.0,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,44,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,45,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,46,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,47,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,48,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,49,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,50,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.0
-#   => PR,51,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,52,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,53,396,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,54,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,55,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,56,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0
-#   => PR,57,396,0.0,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,0.0,99.4949,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,58,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,59,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0
-#   => PR,60,396,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,61,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,62,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,63,396,0.0,0.0,0.0,0.0,0.0,0.0,0.2525,0.0,0.0,37.8788,0.0,0.0,61.8687,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,64,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.1212,0.0,37.8788,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,65,396,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,66,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,67,396,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,68,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,69,396,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,70,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,71,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.1212,37.8788,0.0,0.0,0.0
-#   => PR,72,396,0.0,0.0,0.0,37.8788,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,62.1212,0.0,0.0,0.0,0.0
-#   => PR,73,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,74,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,75,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0
-#   => PR,76,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,77,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,78,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,79,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,80,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,81,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,82,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0
-#   => PR,83,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.4949,0.0,0.0,0.0,0.5051,0.0,0.0,0.0,0.0,0.0
-#   => PR,84,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,85,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,86,396,0.0,0.0,0.0,0.5051,0.0,99.4949,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,87,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,88,396,0.0,0.0,62.1212,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,37.8788,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,89,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,90,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,91,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,92,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,93,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,94,396,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,95,396,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,96,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0
-#   => PR,97,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-#   => PR,98,396,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,99.7475,0.0,0.0,0.0,0.2525,0.0,0.0,0.0,0.0,0.0
-#   => PR,99,396,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-
-
-
-module ViralSeq
-
-  # drug resistant mutation summary. input: amino acid array and starting codon, output, hash of summary
-  def self.sdrm_nrti(aa_array,start_aa=1)
-    out_hash = {}
-    sdrm = {}
-    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"]]
-    aa_length = aa_array.size
-    end_aa = start_aa + aa_length - 1
-    (start_aa..end_aa).each do |position|
-      array_position = position - start_aa
-      if sdrm.keys.include?(position)
-        wt_aa = sdrm[position][0]
-        test_aa = aa_array[array_position]
-        if test_aa.size == 1
-          unless wt_aa == test_aa
-            if sdrm[position][1].include?(test_aa)
-              out_hash[position] = [wt_aa,test_aa]
-            end
-          end
-        else
-          test_aa_array = test_aa.split("/")
-          if (test_aa_array & sdrm[position][1])
-            out_hash[position] = [wt_aa,test_aa]
-          end
-        end
-
-      end
-    end
-    return out_hash
-  end
-
-  def self.sdrm_nnrti(aa_array,start_aa=1)
-    out_hash = {}
-    sdrm = {}
-    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']]
-    aa_length = aa_array.size
-    end_aa = start_aa + aa_length - 1
-    (start_aa..end_aa).each do |position|
-      array_position = position - start_aa
-      if sdrm.keys.include?(position)
-        wt_aa = sdrm[position][0]
-        test_aa = aa_array[array_position]
-        if test_aa.size == 1
-          unless wt_aa == test_aa
-            if sdrm[position][1].include?(test_aa)
-              out_hash[position] = [wt_aa,test_aa]
-            end
-          end
-        else
-          test_aa_array = test_aa.split("/")
-          if (test_aa_array & sdrm[position][1])
-            out_hash[position] = [wt_aa,test_aa]
-          end
-        end
-
-      end
-    end
-    return out_hash
-  end
-
-  #HIV protease surveillance mutations
-
-  def self.hiv_protease(aa_array,start_aa=1)
-    out_hash = {}
-    sdrm = {}
-    sdrm[23] = ['L',['I']]
-    sdrm[24] = ['L',['I']]
-    sdrm[30] = ['D',['N']]
-    sdrm[32] = ['V',['I']]
-    sdrm[46] = ['M',['I','L','V']] # M46V not on the SDRM list but we still include it.
-    sdrm[47] = ['I',['V','A']]
-    sdrm[48] = ['G',['V','M']]
-    sdrm[50] = ['I',['V','L']]
-    sdrm[53] = ['F',['Y']]
-    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[85] = ['I',['V']]
-    sdrm[88] = ['N',['D','S']]
-    sdrm[90] = ['L',['M']]
-    aa_length = aa_array.size
-    end_aa = start_aa + aa_length - 1
-    (start_aa..end_aa).each do |position|
-      array_position = position - start_aa
-      if sdrm.keys.include?(position)
-        wt_aa = sdrm[position][0]
-        test_aa = aa_array[array_position]
-        if test_aa.size == 1
-          unless wt_aa == test_aa
-            if sdrm[position][1].include?(test_aa)
-              out_hash[position] = [wt_aa,test_aa]
-            end
-          end
-        else
-          test_aa_array = test_aa.split("/")
-          if (test_aa_array & sdrm[position][1])
-            out_hash[position] = [wt_aa,test_aa]
-          end
-        end
-      end
-    end
-    return out_hash
-  end
-
-  #HIV integrase drug resistance mutations
-
-  def self.sdrm_int(aa_array,start_aa=1)
-    out_hash = {}
-    sdrm = {}
-    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']]
-    aa_length = aa_array.size
-    end_aa = start_aa + aa_length - 1
-    (start_aa..end_aa).each do |position|
-      array_position = position - start_aa
-      if sdrm.keys.include?(position)
-        wt_aa = sdrm[position][0]
-        test_aa = aa_array[array_position]
-        if test_aa.size == 1
-          unless wt_aa == test_aa
-            if sdrm[position][1].include?(test_aa)
-              out_hash[position] = [wt_aa,test_aa]
-            end
-          end
-        else
-          test_aa_array = test_aa.split("/")
-          if (test_aa_array & sdrm[position][1])
-            out_hash[position] = [wt_aa,test_aa]
-          end
-        end
-
-      end
-    end
-    return out_hash
-  end
-
-  # input sequence hash, and Poisson cutoff for minority variants.
-  # HIV-1 PR region SDRM based on HIVDB.stanford.edu
-  # only for MPID-DR MiSeq sequences, PR codon 1-99
-  # return [substitution rate with 95% CI, halpotype abundance with 95% CI, amino acid sequence report spreadsheet]
-  def self.sdrm_pr_bulk(sequences, cutoff = 0)
-    region = "PR"
-    rf_label = 0
-    start_codon_number = 1
-    n_seq = sequences.size
-    mut = {}
-    mut_com = []
-    aa = {}
-    point_mutation_list = []
-    sequences.each do |name,seq|
-      s = ViralSeq::Sequence.new(name,seq)
-      s.get_aa_array(rf_label)
-      aa_seq = s.aa_array
-      aa[name] = aa_seq.join("")
-      record = ViralSeq.hiv_protease(aa_seq)
-      mut_com << record
-      record.each do |position,mutation|
-        if mut[position]
-          mut[position][1] << mutation[1]
-        else
-          mut[position] = [mutation[0],[]]
-          mut[position][1] << mutation[1]
-        end
-      end
-    end
-    mut.each do |position,mutation|
-      wt = mutation[0]
-      mut_list = mutation[1]
-      count_mut_list = ViralSeq.count(mut_list)
-      count_mut_list.each do |m,number|
-        ci = ViralSeq.r_binom_CI(number, n_seq)
-        label = number < cutoff ? "*" : ""
-        point_mutation_list << [region, n_seq, position, wt, m, number, (number/n_seq.to_f).round(5), ci[0], ci[1], label]
-      end
-    end
-    point_mutation_list.sort_by! {|record| record[2]}
-
-    link = ViralSeq.count(mut_com)
-    link2 = {}
-    link.each do |k,v|
-      pattern = []
-      if k.size == 0
-        pattern = ['WT']
-      else
-        k.each do |p,m|
-          pattern << (m[0] + p.to_s + m[1])
-        end
-      end
-      link2[pattern.join("+")] = v
-    end
-    linkage_list = []
-    link2.sort_by{|_key,value|value}.reverse.to_h.each do |k,v|
-      ci = ViralSeq.r_binom_CI(v, n_seq)
-      label = v < cutoff ? "*" : ""
-      linkage_list << [region, n_seq, k, v, (v/n_seq.to_f).round(5), ci[0], ci[1], label]
-    end
-
-    report_list = []
-
-    div_aa = {}
-    aa_start = start_codon_number
-
-    aa_size = aa.values[0].size - 1
-
-    (0..aa_size).to_a.each do |p|
-      aas = []
-      aa.values.each do |r1|
-        aas << r1[p]
-      end
-      count_aas = ViralSeq.count(aas)
-      div_aa[aa_start] = count_aas.sort_by{|_k,v|v}.reverse.to_h
-      aa_start += 1
-    end
-
-    div_aa.each do |k,v|
-      record = [region, k, n_seq]
-      ViralSeq::AMINO_ACID_LIST.each do |amino_acid|
-        aa_count = v[amino_acid]
-        record << (aa_count.to_f/n_seq*100).round(4)
-      end
-      report_list << record
-    end
-
-    return [point_mutation_list, linkage_list, report_list]
-  end
-
-
-  #input sequence hash, and Poisson cutoff for minority variants.
-  #HIV-1 RT region SDRM based on HIVDB.stanford.edu
-  #only for MPID-DR MiSeq sequences
-  #RT codon 34-122, 152-236 two regions are linked.
-  #return [substitution rate with 95% CI, halpotype abundance with 95% CI, amino acid sequence report spreadsheet]
-  def self.sdrm_rt_bulk(sequences, cutoff = 0)
-    region = "RT"
-    rf_label = 1
-    start_codon_number = 34
-    gap = "AGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCAC"
-
-    n_seq = sequences.size
-    mut_nrti = {}
-    mut_nnrti = {}
-    mut_com = []
-    r1_aa = {}
-    r2_aa = {}
-    point_mutation_list = []
-    sequences.each do |name,seq|
-      r1 = seq[0,267]
-      r2 = seq[267..-1]
-      seq = r1 + gap + r2
-      s = ViralSeq::Sequence.new(name,seq)
-      s.get_aa_array(rf_label)
-      aa_seq = s.aa_array
-
-      r1_aa[name] = aa_seq[0,89].join("")
-      r2_aa[name] = aa_seq[-85..-1].join("")
-      nrti = ViralSeq.sdrm_nrti(aa_seq,start_codon_number)
-      nnrti = ViralSeq.sdrm_nnrti(aa_seq,start_codon_number)
-      mut_com << (nrti.merge(nnrti))
-
-      nrti.each do |position,mutation|
-        if mut_nrti[position]
-          mut_nrti[position][1] << mutation[1]
-        else
-          mut_nrti[position] = [mutation[0],[]]
-          mut_nrti[position][1] << mutation[1]
-        end
-      end
-      nnrti.each do |position,mutation|
-        if mut_nnrti[position]
-          mut_nnrti[position][1] << mutation[1]
-        else
-          mut_nnrti[position] = [mutation[0],[]]
-          mut_nnrti[position][1] << mutation[1]
-        end
-      end
-    end
-
-    mut_nrti.each do |position,mutation|
-      wt = mutation[0]
-      mut_list = mutation[1]
-      count_mut_list = ViralSeq.count(mut_list)
-      count_mut_list.each do |m,number|
-        ci = ViralSeq.r_binom_CI(number, n_seq)
-        label = number < cutoff ? "*" : ""
-        point_mutation_list << ["NRTI", n_seq, position, wt, m, number, (number/n_seq.to_f).round(5), ci[0], ci[1], label]
-      end
-    end
-
-    mut_nnrti.each do |position,mutation|
-      wt = mutation[0]
-      mut_list = mutation[1]
-      count_mut_list = ViralSeq.count(mut_list)
-      count_mut_list.each do |m,number|
-        ci = ViralSeq.r_binom_CI(number, n_seq)
-        label = number < cutoff ? "*" : ""
-        point_mutation_list << ["NNRTI", n_seq, position, wt, m, number, (number/n_seq.to_f).round(5), ci[0], ci[1], label]
-      end
-    end
-    point_mutation_list.sort_by! {|record| record[2]}
-
-    link = ViralSeq.count(mut_com)
-    link2 = {}
-    link.each do |k,v|
-      pattern = []
-      if k.size == 0
-        pattern = ['WT']
-      else
-        k.each do |p,m|
-          pattern << (m[0] + p.to_s + m[1])
-        end
-      end
-      link2[pattern.join("+")] = v
-    end
-    linkage_list = []
-    link2.sort_by{|_key,value|value}.reverse.to_h.each do |k,v|
-      ci = ViralSeq.r_binom_CI(v, n_seq)
-      label = v < cutoff ? "*" : ""
-      linkage_list << [region, n_seq, k, v, (v/n_seq.to_f).round(5), ci[0], ci[1], label]
-    end
-
-    report_list = []
-
-    div_aa = {}
-    r1_aa_start = 34
-    r2_aa_start = 152
-
-    r1_aa_size = r1_aa.values[0].size - 1
-    r2_aa_size = r2_aa.values[0].size - 1
-
-    (0..r1_aa_size).to_a.each do |p|
-      aas = []
-      r1_aa.values.each do |r1|
-        aas << r1[p]
-      end
-      count_aas = ViralSeq.count(aas)
-      div_aa[r1_aa_start] = count_aas.sort_by{|_k,v|v}.reverse.to_h
-      r1_aa_start += 1
-    end
-
-    (0..r2_aa_size).to_a.each do |p|
-      aas = []
-      r2_aa.values.each do |r1|
-        aas << r1[p]
-      end
-      count_aas = ViralSeq.count(aas)
-      div_aa[r2_aa_start] = count_aas.sort_by{|_k,v|v}.reverse.to_h
-      r2_aa_start += 1
-    end
-
-    div_aa.each do |k,v|
-      record = [region, k, n_seq]
-      ViralSeq::AMINO_ACID_LIST.each do |amino_acid|
-        aa_count = v[amino_acid]
-        record << (aa_count.to_f/n_seq*100).round(4)
-      end
-      report_list << record
-    end
-
-    return [point_mutation_list, linkage_list, report_list]
-  end
-
-  #input sequence hash, and Poisson cutoff for minority variants.
-  #HIV-1 IN region SDRM based on HIVDB.stanford.edu
-  #only for MPID-DR MiSeq sequences
-  #IN codon 53-174
-  #return [substitution rate with 95% CI, halpotype abundance with 95% CI, amino acid sequence report spreadsheet]
-  def self.sdrm_in_bulk(sequences, cutoff = 0)
-    region = "IN"
-    rf_label = 2
-    start_codon_number = 53
-    n_seq = sequences.size
-    mut = {}
-    mut_com = []
-    aa = {}
-    point_mutation_list = []
-    sequences.each do |name,seq|
-      s = ViralSeq::Sequence.new(name,seq)
-      s.get_aa_array(rf_label)
-      aa_seq = s.aa_array
-      aa[name] = aa_seq.join("")
-      record = ViralSeq.sdrm_int(aa_seq, start_codon_number)
-      mut_com << record
-      record.each do |position,mutation|
-        if mut[position]
-          mut[position][1] << mutation[1]
-        else
-          mut[position] = [mutation[0],[]]
-          mut[position][1] << mutation[1]
-        end
-      end
-    end
-    mut.each do |position,mutation|
-      wt = mutation[0]
-      mut_list = mutation[1]
-      count_mut_list = ViralSeq.count(mut_list)
-      count_mut_list.each do |m,number|
-        ci = ViralSeq.r_binom_CI(number, n_seq)
-        label = number < cutoff ? "*" : ""
-        point_mutation_list << [region, n_seq, position, wt, m, number, (number/n_seq.to_f).round(5), ci[0], ci[1], label]
-      end
-    end
-    point_mutation_list.sort_by! {|record| record[2]}
-
-    link = ViralSeq.count(mut_com)
-    link2 = {}
-    link.each do |k,v|
-      pattern = []
-      if k.size == 0
-        pattern = ['WT']
-      else
-        k.each do |p,m|
-          pattern << (m[0] + p.to_s + m[1])
-        end
-      end
-      link2[pattern.join("+")] = v
-    end
-    linkage_list = []
-    link2.sort_by{|_key,value|value}.reverse.to_h.each do |k,v|
-      ci = ViralSeq.r_binom_CI(v, n_seq)
-      label = v < cutoff ? "*" : ""
-      linkage_list << [region, n_seq, k, v, (v/n_seq.to_f).round(5), ci[0], ci[1], label]
-    end
-
-    report_list = []
-
-    div_aa = {}
-    aa_start = start_codon_number
-
-    aa_size = aa.values[0].size - 1
-
-    (0..aa_size).to_a.each do |p|
-      aas = []
-      aa.values.each do |r1|
-        aas << r1[p]
-      end
-      count_aas = ViralSeq.count(aas)
-      div_aa[aa_start] = count_aas.sort_by{|_k,v|v}.reverse.to_h
-      aa_start += 1
-    end
-
-    div_aa.each do |k,v|
-      record = [region, k, n_seq]
-      ViralSeq::AMINO_ACID_LIST.each do |amino_acid|
-        aa_count = v[amino_acid]
-        record << (aa_count.to_f/n_seq*100).round(4)
-      end
-      report_list << record
-    end
-
-    return [point_mutation_list, linkage_list, report_list]
-  end
-
-end