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ghetto_blaster

Invoke comme ca,

ruby ghetto_blaster.rb query.fa database.fa

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]
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