ghetto_blaster

readme.md

Invoke comme ca,

ruby ghetto_blaster.rb query.fa database.fa

ghetto_blaster.rb

LEVEL = 9

database = ARGV[0]
query = ARGV[1]

require 'zlib'

# Compression function.
def deflate(string)
   z = Zlib::Deflate.new(LEVEL)
   dst = z.deflate(string, Zlib::FINISH)
   z.close
   dst
end

# Load entire database into memory.
db = Hash.new
File.new(database).read.split(/^>/).each do |record|
  next if record == "" # split makes a blank one for some reason
  record = record.split("\n")
  header, sequence = record[0], record[1..-1]
  db[header] = sequence.join('')
end

# Read query sequence, and compress.
query_sequence = \
  File.new(query).read.split(/^>/)[1].split("\n")[1..-1].join('') # :D


# Find database sequence is greatest reduction in size

def query(query, db)
  query_size = deflate(query).length
  best, winner = 0, ''
  
  db.each do |k, seq|
    # Compress DB sequence
    solo = deflate(seq).length
  
    # Compress both, together
    together = deflate(seq + query).length
    
    # Score
    if together < (solo + query_size)
      score = (solo + query_size - together)/seq.length.to_f # Normalize by subject length
      if score > best
        best = score
        winner = k
      end
    end
    
  end
  {:score => best, :hit => winner}
end

result = query(query_sequence, db)
puts result[:hit]