Module: BioLocus::Keys

Defined in:
lib/bio-locus/locus.rb

Constant Summary collapse

@@in_list = 
{}

Class Method Summary collapse

Class Method Details

.each_key(line, options) ⇒ Object 



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# File 'lib/bio-locus/locus.rb', line 6

def Keys::each_key(line,options)
  use_alt = (options[:alt] == :include or options[:alt] == :only)
  use_pos = (options[:alt] == :include or options[:alt] == :exclude)

  if line =~ /^[[:alnum:]]+/
    fields = nil
    # The default layout (VCF) may or may not work. Critically
    # chr,pos and alt are expected in positions 0,1,4 respectively.
    chr,pos,id,no_use,alt,rest = line.split(/\t/,6)[0..-1]
    if options[:in_format] or options[:eval_chr] or options[:eval_pos] or options[:eval_alt]
      fields = line.split(/\t/)
      field = fields
      case options[:in_format]
        when :tab then
          # chr,pos,ref,alt
          alt = field[3].strip.split(/,/)[0] if field[3]
        when :snv then
          alt = field[2].split(/\//)[1] if field[2]
        when :cosmic then
          # COSMIC tsv files, either in field 17 (COSMICv70)
          locus_field = field[17]
          locus_field = field[13] if locus_field !~ /:/
          if field[15] !~ /delet/i and locus_field =~ /:/
            chr = /^([^:]+)/.match(locus_field)[1]
            a = /:(\d+)-(\d+)/.match(locus_field)
            pos = a[1] if a[1]==a[2]
          end
      end
      # Override parsing with
      if options[:eval_chr]
        chr = eval(options[:eval_chr])
      end
      if options[:eval_pos] 
        pos = eval(options[:eval_pos])
      end
      if options[:eval_alt] 
        alt = eval(options[:eval_alt])
      end
    end
    # p [:debug,chr,pos,alt] if options[:debug]

    # If we have a position emit it
    if pos =~ /^\d+$/ and chr and chr != ''
      alts = if use_pos
               ['']  
             else
               []
             end
      alts += alt.split(/,/) if use_alt and alt
      alts.each do | nuc |
        key = chr+"\t"+pos
        key += "\t"+nuc if nuc != ''
        if options[:once]
          # check we haven't already sent this out in this run
          return if @@in_list[key]
          @@in_list[key] = true
        end
        yield key
      end
    else
      if options[:ignore_errors]
        $stderr.print "WARNING, <#{chr}:#{pos}> skipping: ",line if not options[:quiet]
      else
        p line
        p fields
        raise "Parse error chr <#{chr}> pos <#{pos}>\n"
      end
    end
  end
end