Class: Cytogenetics::Karyotype

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

Constant Summary collapse

@@haploid = 
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Class Attribute Summary collapse

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(karyotype_str) ⇒ Karyotype

Returns a new instance of Karyotype.

Raises:

  • (ArgumentError) 


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# File 'lib/cytogenetics/karyotype.rb', line 17

def initialize(karyotype_str)
  config_logging()
  raise ArgumentError, "#{karyotype_str} is not a karyotype." unless (karyotype_str.is_a? String and karyotype_str.length > 1)
  @log.info("Reading karyotype #{karyotype_str}")

  @karyotype = karyotype_str.gsub(/\s/, "")
  @original_karyotype = @karyotype # just to keep it around before it gets cleaned up
  @normal_chr = {}; @abnormal_chr = {}; @aberrations = {}; @unclear_aberrations = [];
  setup_abberation_objs()
  prep_karyotype()
  handle_ploidy_diff()
  analyze()
end

Class Attribute Details

.aberration_objs ⇒ Object

Returns the value of attribute aberration_objs.



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# File 'lib/cytogenetics/karyotype.rb', line 14

def aberration_objs
  @aberration_objs
end

.log ⇒ Object

Returns the value of attribute log.



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# File 'lib/cytogenetics/karyotype.rb', line 14

def log
  @log
end

.unclear_aberrations ⇒ Object

Returns the value of attribute unclear_aberrations.



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# File 'lib/cytogenetics/karyotype.rb', line 14

def unclear_aberrations
  @unclear_aberrations
end

Instance Attribute Details

#aberrations ⇒ Object (readonly)

Returns the value of attribute aberrations.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def aberrations
  @aberrations
end

#abnormal_chr ⇒ Object (readonly)

Returns the value of attribute abnormal_chr.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def abnormal_chr
  @abnormal_chr
end

#karyotype ⇒ Object (readonly)

Returns the value of attribute karyotype.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def karyotype
  @karyotype
end

#normal_chr ⇒ Object (readonly)

Returns the value of attribute normal_chr.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def normal_chr
  @normal_chr
end

#original_karyotype ⇒ Object (readonly)

Returns the value of attribute original_karyotype.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def original_karyotype
  @original_karyotype
end

#ploidy ⇒ Object (readonly)

Returns the value of attribute ploidy.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def ploidy
  @ploidy
end

#sex ⇒ Object (readonly)

Returns the value of attribute sex.



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# File 'lib/cytogenetics/karyotype.rb', line 11

def sex
  @sex
end

Instance Method Details

#analyze ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 31

def analyze
  Aberration.aberration_type.each do |abr_type|
    next unless @aberrations.has_key? abr_type
    regex = @aberration_obj[abr_type].regex

    @aberrations[abr_type].each do |abr|
#        if abr_type
      abr.match(regex)
      @log.warn("Aberration has two chromosomes #{abr} but only the first one is handled.") unless ($2.nil? or $1.eql? $2)

      ## TODO deal with the case of 2 chromosomes defined in the aberration
      chr = Chromosome.new($1, true)
      chr.aberration(@aberration_obj[abr_type].new(abr))

      @abnormal_chr[chr.name] = [] unless @abnormal_chr.has_key? chr.name
      @abnormal_chr[chr.name] << chr
    end
  end
end

#config_logging ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 102

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

#handle_ploidy_diff ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 113

def handle_ploidy_diff
  @aberrations[:loss].each { |c| @normal_chr[c] -= 1 } if @aberrations[:loss]
  @aberrations[:gain].each { |c| @normal_chr[c] += 1 } if @aberrations[:gain]
end

#prep_karyotype ⇒ Object

determine ploidy & gender, clean up each aberration and drop any “unknown”



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# File 'lib/cytogenetics/karyotype.rb', line 119

def prep_karyotype
  @karyotype.gsub!(/\s/, "")
  clones = @karyotype.scan(/(\[\w+\])/).collect { |a| a[0] }
  @log.warn("Karyotype is a collection of clones, analysis may be inaccurate.") if clones.length > 3

  @karyotype.gsub!(/\[\w+\]/, "") # don't care about numbers of cells: [5] or [cp10], there are some other problematic things in [] but they are just being ignored currently

  (pl, sc) = @karyotype.split(",")[0..1]
  if (pl and sc)
    @ploidy = KaryotypeReader.calculate_ploidy(pl, @@haploid)
    sex_chr = KaryotypeReader.determine_sex(sc)
  else
    raise KaryotypeError, "'#{@karyotype}' is not a valid karyotype. Ploidy and sex defnitions are absent"
  end

  st = sex_chr.values.inject { |sum, v| sum+v }
  @sex = nil
  karyotype_index = 1 # sometimes the sex is not indicated and there's no case information to figure it out
  if st > 0
    @sex = sex_chr.keys.join("")
    karyotype_index = 2
  end

  (Array(1..23)).each { |c| @normal_chr[c.to_s] = @ploidy.to_i }

  sex_chr.each_pair { |c, p| @normal_chr[c] = p.to_i }

  # deal with the most common karyotype string inconsistencies
  cleaned_karyotype = []

  @karyotype.split(",")[karyotype_index..-1].each do |abr|
    cleaned_karyotype |= [cleaned_karyotype, KaryotypeReader.cleanup(abr)].flatten
  end
  @karyotype = cleaned_karyotype

  # classify each type of aberration in the karyotype
  @karyotype.each do |k|
    abrclass = Aberration.classify_aberration(k)
    @aberrations[abrclass] = [] unless @aberrations.has_key? abrclass
    @aberrations[abrclass] << k.sub(/^(\+|-)?/, "")
  end

  @aberrations.each_pair do |abrclass, abrlist|
    next if (abrclass.eql? ChromosomeAberrations::ChromosomeGain.type or abrclass.eql? ChromosomeAberrations::ChromosomeLoss.type)
    # aberrations other than chromosome gains/losses should be uniquely represented

    counts = abrlist.inject(Hash.new(0)) { |h, i| h[i] += 1; h }
    counts.each_pair { |k, v| @log.warn("#{k} was seen multiple times. Analyzed only once.") if v > 1 }

    @aberrations[abrclass] = abrlist.uniq
  end

end

#report_breakpoints ⇒ Object

get breakpoints for the karyotype



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# File 'lib/cytogenetics/karyotype.rb', line 52

def report_breakpoints
  bps = Array.new
  @abnormal_chr.each_pair do |c, chr_list|
    chr_list.each do |chr|
      bps << chr.breakpoints
    end
  end
  bps.delete_if { |c| c.empty? }
  bps.flatten!
  return bps
end

#report_fragments ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 64

def report_fragments
  frags = []
  @abnormal_chr.each_pair do |c, chr_list|
    chr_list.each do |chr|
      frags << chr.fragments
    end
  end
  frags.delete_if { |c| c.empty? }
  frags.flatten!
  return frags
end

#report_ploidy_change ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 76

def report_ploidy_change
  pd = []
  pd << @aberrations[:loss].map { |e| "-#{e}" } if @aberrations[:loss]
  pd << @aberrations[:gain].map { |e| "+#{e}" } if @aberrations[:gain]
  pd.flatten!
  return pd
end

#setup_abberation_objs ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 108

def setup_abberation_objs
  @aberration_obj = Aberration.aberration_objs
end

#summarize ⇒ Object 



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# File 'lib/cytogenetics/karyotype.rb', line 84

def summarize
  summary = "NORMAL CHROMOSOMES\n"
  @normal_chr.each_pair do |chr, count|
    summary = "#{summary} #{chr}: #{count}\n"
  end

  summary = "#{summary}\nABNORMAL:"
  @abnormal_chr.each_pair do |chr, list|
    summary = "#{summary}\n#{chr}"
    list.each do |c|
      summary = "#{summary}\n#{c.aberrations}\n"
      summary = "#{summary}\n#{c.breakpoints}\n"
    end
  end
end