Class: Cytogenetics::KaryotypeReader

Inherits:
Object
  • Object
show all
Defined in:
lib/cytogenetics/utils/karyotype_reader.rb

Class Method Summary collapse

Class Method Details

.calculate_ploidy(str, haploid) ⇒ Object 



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# File 'lib/cytogenetics/utils/karyotype_reader.rb', line 72

def self.calculate_ploidy(str, haploid)
  config_logging

  str.sub!(/<.{2,}>/, "")
  str = $1 if str.match(/\d+\((\d+-\d+)\)/)

  diploid = haploid*2
  triploid = haploid*3
  quadraploid = haploid*4

  # typically see di- tri- quad- if more than that it should be noted
  ploidy = nil
  min = diploid
  max = diploid
  #if str.match(/<\+(\d)n>/) # sometimes see this odd configuration: 46<+3n>
  #  ploidy = $1
  if str.match(/(\d+)[-|~](\d+)/) # num and range or just range: 46-53
    min = $1.to_i; max = $2.to_i
  elsif str.match(/^(\d+)/) # single num:  72
    min = $1.to_i; max = $1.to_i
  end

  if min < haploid
    @log.warn("Ploidy determination may be bad as the min was less than haploid (#{str}). Setting to haploid.")
    min = haploid
  end

  if ploidy.nil?
    case
      when (min.eql? diploid and max.eql? diploid)
        @log.debug("Normal ploidy: #{str}")
        ploidy = 2
      when ((min >= haploid and max <= diploid) or (min <= diploid and max < triploid))
        @log.debug("Relatively normal ploidy #{str}")
        ploidy = 2
      when (min >= haploid and max < quadraploid)
        @log.debug("Triploid #{str}")
        ploidy = 3
      when (max >= quadraploid)
        @log.debug("Quadraploid #{str}")
        ploidy = 4
      else
        raise KaryotypeError, "Failed to determine ploidy for #{str}"
    end
  end
  return ploidy
end

.cleanup(abr) ⇒ Object 



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# File 'lib/cytogenetics/utils/karyotype_reader.rb', line 11

def self.cleanup(abr)
  config_logging

  new_abr = []

  # +t(13;X)(q13;p12) doesn't need a +
  abr.sub!(/^[\+|-]/, "") unless abr.match(/^[\+|-][\d|X|Y]+$/)

  # not going to bother with aberrations that are unclear/unknown '?' or with '**'
  if (abr.match(/\?|\*\*/))
    @log.warn("Removing aberration with unknown/unclear information: #{abr}")
    return new_abr
  end

  # 13x2 is normal, 13x3 is a duplicate and should read +13
  if abr.match(/^([\d+|X|Y]+)x(\d+)/)
    chr = $1; dups = $2.to_i
    if dups.eql? 0 # managed to lose both chromosomes in a diploidy karyotype
      (Array(1..dups)).map { new_abr.push("-#{chr}") }
    elsif dups > 2 # sometimes you have 13x3, really just means 1 additional chr 13 since normal ploidy is 2
      dups -= 2
      (Array(1..dups)).map { new_abr.push("+#{chr}") }
    elsif dups.eql?(1)
      new_abr.push("-#{chr}")
    end
    # add(9)(p21)x2 or add(7)x2 should indicate that this "additional material of unk origin" happened twice
  elsif abr.match(/(.*)x(\d+)$/)
    a = $1; dups = $2.to_i
    (Array(1..dups)).map { new_abr.push(a) }
    # del(7) should be -7  but not del(7)(q12)
  else # everything else
    new_abr.push(abr)
  end

  return new_abr
end

.config_logging ⇒ Object 



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# File 'lib/cytogenetics/utils/karyotype_reader.rb', line 5

def self.config_logging
  @log = Cytogenetics.logger
  #@log.progname = self.name
end

.determine_sex(str) ⇒ Object 



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# File 'lib/cytogenetics/utils/karyotype_reader.rb', line 48

def self.determine_sex(str)
  config_logging

  sex_chr = {}
  ['X', 'Y'].each { |c| sex_chr[c] = 0 }

  unless str.match(/^(X|Y)+$/)
    @log.warn("Definition of gender incorrect (#{str})")
  else
    #raise KaryotypeError, "Definition of gender incorrect (#{str})" unless str.match(/^(X|Y)+$/)
    # ploidy number makes no difference since this string will tell us how many or at least what the gender should be

    chrs = str.match(/([X|Y]+)/).to_s.split(//)
    chrs.each { |c| sex_chr[c] +=1 }

    # assume this was an XY karyotype that may have lost the Y, have only seen this in
    # severely affected karyotypes NOT TRUE, some karyotypes are just not defined correctly
    # often XX -X is listed as X,...  Cannot assume it's a male missing Y
    #sex_chr['Y'] += 1 if (chrs.length.eql?(1) and chrs[0].eql?('X'))
  end

  return sex_chr
end