Module: BioLocus::Match

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

Class Method Summary collapse

Class Method Details

.run(options) ⇒ Object 



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# File 'lib/bio-locus/match.rb', line 3

def Match.run(options)
  do_delete = (options[:task] == :delete)
  invert_match = options[:invert_match]
  store = DbMapper.factory(options)
  lines = 0 
  header_lines = 0
  count = 0
  in_header = true
  uniq_match = {}
  uniq_no_match = {}
  STDIN.each_line do | line |
    if in_header and line =~ /^#/
      # Retain comments in header (for VCF)
      print line
      header_lines += 1
      next
    else
      in_header = false
    end
    if line =~ /^#/
      header_lines += 1
    else
      lines += 1
    end
    $stderr.print '.' if (lines % 1_000_000) == 0 if not options[:quiet]
    Keys::each_key(line,options) do | key |
      has_match = lambda { 
                           if invert_match
                             not store[key]
                           else
                             store[key]
                           end
                         }
      if has_match.call
        # We have a match
        $stderr.print "Matched <#{key}>\n" if options[:debug]
        count += 1
        if do_delete
          store.delete(key)
        else
          print line
          uniq_match[key] ||= true
        end
      else
        uniq_no_match[key] ||= true
      end
    end
  end
  store.close
  if do_delete
    $stderr.print "\nDeleted #{count} keys in #{options[:db]} reading #{lines} lines !\n" if not options[:quiet]
  else
    $stderr.print "\nMatched #{count} (unique #{uniq_match.keys.size}) lines out of #{lines} (header #{header_lines}, unique #{uniq_no_match.keys.size+uniq_match.keys.size}) in #{options[:db]}!\n" if not options[:quiet]
  end
end