from Bio import motifs
from Bio import SeqIO
from Bio.Alphabet.IUPAC import unambiguous_dna

import sys

seq, motif = sys.argv[1:3]

m = motifs.parse(open(motif), 'meme')[0]

m.pseudocounts = 0.01
    
distribution = m.pssm.distribution()
score_t = distribution.threshold_fnr(0.1)
    
pssm = m.pssm

s = SeqIO.read(open(seq), 'fasta')
s.seq.alphabet = unambiguous_dna
for position, score in pssm.search(s.seq, threshold=score_t):
	print position, score