Comments on: Obtaining overrepresented motifs in DNA sequences, part 13 http://python.genedrift.org/2008/08/20/obtaining-overrepresented-motifs-in-dna-sequences-part-13/ a step-by-step guide to create Python applications in bioinformatics Mon, 22 Feb 2010 18:22:18 +0000 http://wordpress.org/?v=3.0-alpha hourly 1 By: Andrew Dalke http://python.genedrift.org/2008/08/20/obtaining-overrepresented-motifs-in-dna-sequences-part-13/comment-page-1/#comment-18180 Andrew Dalke Sun, 24 Aug 2008 15:11:58 +0000 http://python.genedrift.org/?p=149#comment-18180 The code doesn't use the id_no inside of each quorum set, only the length of each set. If you don't need that number then you can use a counter instead of of a set, as in: def get_quorums(seqs, mlen): __quorum = defaultdict(int) __for seq in seqs: ____for n in range(len(seq) - mlen): ______quorum[seq[n:n + mlen]] += 1 __return quorum and replace the main code with for i in foreground: __term1 = choose(background[i], foreground[i]) __term2 = choose((N - background[i]), len(input_seqs)-1) __term3 = choose(N, len(input_seqs)) __p = (float(term1) * float(term2)) / term3 __if 0 < p <= 0.0001: ____print i, foreground[i], background[i], p The code doesn’t use the id_no inside of each quorum set, only the length of each set. If you don’t need that number then you can use a counter instead of of a set, as in:

def get_quorums(seqs, mlen):
__quorum = defaultdict(int)
__for seq in seqs:
____for n in range(len(seq) – mlen):
______quorum[seq[n:n + mlen]] += 1
__return quorum

and replace the main code with

for i in foreground:
__term1 = choose(background[i], foreground[i])
__term2 = choose((N – background[i]), len(input_seqs)-1)
__term3 = choose(N, len(input_seqs))
__p = (float(term1) * float(term2)) / term3
__if 0 < p <= 0.0001:
____print i, foreground[i], background[i], p

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