def main():
parser = optparse.OptionParser(usage="usage: %prog [options] <file>",
description=__doc__)
parser.add_option("-r", "--reverse", action="store_true",
dest="reverse",
help="reverse the sequences, instead of shuffling")
parser.add_option("-m", "--markov", type="int", dest="markov_length",
help="generate Markov sequences, with memory of length"
" N, instead of shuffling", default=None, metavar="N")
parser.add_option("-s", "--seed", type="int", dest="seed",
help="seed for randomness [default 0]",
default=0, metavar="N")
parser.add_option("-n", "--no-original", action="store_true",
dest="no_original",
help="don't output original sequences")
parser.add_option("-v", "--verbose", action="store_true",
dest="verbose", help="be verbose")
DEFAULT_WRAP = 80
parser.add_option("-w", "--wrap", dest="wrap", type="int",
default=DEFAULT_WRAP,
help="wrap sequence to specified width"
" [default %s, 0 means don't wrap at all]" % DEFAULT_WRAP,
metavar="COLUMNS")
parser.add_option("--copyright", action="store_true", dest="copyright",
help="print copyright and exit")
(options, args) = parser.parse_args()
if (len(args) != 1
or options.markov_length != None and options.reverse
or options.markov_length != None and options.markov_length < 0):
parser.print_help()
sys.exit(1)
if options.markov_length != None:
decoy_maker = markov_decoy_maker(options.seed, options.markov_length,
args[0])
elif options.reverse:
decoy_maker = reverse_decoy_maker()
else:
decoy_maker = shuffle_decoy_maker(options.seed)
# locus id -> (defline, hash of sequence)
seen = {}
# real and decoy 6-mers seen
sixmers = (set(), set())
for locusname, defline, sequence, filename \
in greylag.read_fasta_files([args[0]]):
write_locus(options, decoy_maker, seen, sixmers,
locusname, defline, sequence)
common_sixmers = sixmers[0] & sixmers[1]
print >> sys.stderr, ("six-mers: %s real %s decoy %s both"
% (len(sixmers[0]) - len(common_sixmers),
len(sixmers[1]) - len(common_sixmers),
len(common_sixmers)))
def __init__(self, random_seed, length, original_sequence_file):
random.seed(random_seed)
self.length = length
# for order 0 through self.length:
# [ length-mer -> subsequent residues -> count, ... ]
self.transition = [ defaultdict(lambda: defaultdict(int))
for i in range(length+1) ]
for locusname, defline, sequence, filename \
in greylag.read_fasta_files([original_sequence_file]):
for order in range(length+1):
seq = '-' * order + sequence
for i in xrange(len(sequence)):
self.transition[order][seq[i:i+order]][seq[i+order]] += 1
