Class: Cytogenetics::ChromosomeAberrations::Derivative

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

Overview

DERIVATIVE

Instance Attribute Summary

Attributes inherited from Aberration

#ab_objs, #abr, #breakpoints, #fragments

Instance Method Summary collapse

Methods inherited from Aberration

aberration_objs, aberration_type, all_regex, classify_aberration, #config_logging, #find_bands, #find_chr, #find_fragments, #initialize, instantiate_aberrations, regex, #remove_breakpoint, #to_s, type

Constructor Details

This class inherits a constructor from Cytogenetics::Aberration

Instance Method Details

#add_fragments(tbp_list) ⇒ Object

have to reorder the array and then turn Breakpoints into fragments



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# File 'lib/cytogenetics/chromosome_aberrations.rb', line 118

def add_fragments(tbp_list)
  sorted = []
  tbp_list.each_with_index do |e, i|
    if i <= 1
      sorted << Breakpoint.new(e.chr, "#{e.arm}ter") if i.eql? 0
      sorted << e
    elsif i%2 == 0
      sorted << tbp_list[i+1]
      sorted << tbp_list[i]
    end
  end
  sorted << Breakpoint.new(sorted[-1].chr, "#{sorted[-1].arm}ter")
  sorted.each_slice(2).to_a.each do |pair|
    @fragments << Fragment.new(pair[0], pair[1])
  end
end

#get_breakpoints ⇒ Object 



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# File 'lib/cytogenetics/chromosome_aberrations.rb', line 78

def get_breakpoints
  @aberrations = []

  ab_objs = Aberration.aberration_objs

  chr_i = find_chr(@abr)
  derivative_abr = @abr[chr_i[:end_index]+1..@abr.length]

  # separate different abnormalities within the derivative chromosome and clean it up to make it parseable
  abnormalities = derivative_abr.scan(/([^\(\)]+\(([^\(\)]|\)\()*\))/).collect { |a| a[0] }

  trans_bps = []
  abnormalities.each do |abn|
    abrclass = Aberration.classify_aberration(abn)

    if abrclass.to_s.eql? 'unk' # not dealing with unknowns
      @log.warn("Cannot handle #{abn}, incorrect format.")
      next
    end

    # special handling because translocations are written as a sliding window
    # translocations should also only every have 2 breakpoints...
    if abrclass.to_s.eql? ChromosomeAberrations::Translocation.type
      trans = ChromosomeAberrations::Translocation.new(abn)
      trans_bps << trans.breakpoints
      @breakpoints << trans.breakpoints
    else
      ab_obj = ab_objs[abrclass].new(abn)
      if ab_obj.breakpoints.length > 0
        @aberrations << ab_obj
        @breakpoints << ab_obj.breakpoints
      end
    end
  end
  trans_bps.delete_if { |c| c.empty? }
  add_fragments(trans_bps.flatten!) if trans_bps.length > 0
end