Module: Bio::PolyploidTools::Mask

Defined in:
lib/bio/PolyploidTools/Mask.rb

Class Method Summary collapse

Class Method Details

.find_end(seqs) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Mask.rb', line 14

def self.find_end(seqs)
  size = seqs.values[0].size
  names = seqs.keys
  i = size - 1
  gap_count = 3
  while i > 0 and gap_count > 0
    gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1:0  }.inject(0, :+)
    i -= 1
  end
  i + 1
end

.find_start(seqs) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Mask.rb', line 26

def self.find_start(seqs)
  size = seqs.values[0].size
  names = seqs.keys
  i = 0
  gap_count = 3
  while i < size  and gap_count > 0
    gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1 : 0  } .inject(0, :+)

    i += 1
  end
  i - 1
end

.get(seqs, target: nil, seq_start: 0, seq_end: 0) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Mask.rb', line 39

def self.get(seqs, target: nil, seq_start: 0, seq_end: 0)
  names = seqs.keys
  target = names[0] if target.nil?
  masked_snps = seqs[target].downcase
  i = 0
  while i < masked_snps.size
    different = 0
    cov = 0
    gap = false
    names.each do | chr |
      if seqs[chr][i]  != "-" and seqs[chr][i]  != "n" and seqs[chr][i]  != "N"
        cov += 1
      end
      if chr != target
       different += 1  if masked_snps[i].upcase != seqs[chr][i].upcase
      end
      if seqs[chr][i]  == "-" and chr == target
          gap = true
      end
    end
    masked_snps[i] = "." if different == 0
    masked_snps[i] = "." if cov == 1
    masked_snps[i] = "*" if cov == 0
    expected_snps  = names.size - 1
    masked_snps[i] = masked_snps[i].upcase if different == expected_snps
    if gap
      masked_snps[i] = different == expected_snps ? "-" : "_"
    end
    masked_snps[i] = "|" if i < seq_start or i > seq_end
    i += 1
  end
  masked_snps
end

.stats(mask, triad, gene, genome, reference) ⇒ Object 



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# File 'lib/bio/PolyploidTools/Mask.rb', line 73

def self.stats(mask, triad, gene, genome, reference)
  specific = []
  semispecific = []
  sp_i = 0
  semi = 0
  i = 0
  mask.to_s.each_char do |e|
    case e
    when "n","N"
      i += 1
    when /[[:lower:]]/ then
      semispecific << semi
      semi = 0
      i += 1
    when /[[:upper:]]/ then
      specific     << sp_i
      semispecific << semi
      sp_i = 0
      semi = 0
      i += 1
    when "." then
      semi += 1
      sp_i += 1
      i += 1
    end
  end
  {
    reference: reference,
    triad: triad,
    genome: genome,
    gene: gene,
    semispecific_mean: semispecific.mean,
    semispecific_bases: semispecific.size,
    semispecific_identity: (1 - (semispecific.size.to_f / i)) * 100 ,
    specific_mean: specific.mean,
    specific_bases: specific.size,
    specific_identity: (1 - (specific.size.to_f / i )) * 100,
    aligned_length: i,
    specific: specific,
    semispecific: semispecific
  }
end