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src/s/t/STEME-1.8.23/python/stempy/planted_sites.py   STEME(Download)
def parse_meme_output_for_sites(meme_output):
    "Parse MEME-like output"
    logging.info('Parsing predictions from %s', meme_output)
    predicted_sites = defaultdict(P.IntIntervalSet)
    motifs = list(Motif.parse(open(meme_output), "MEME"))

src/s/t/STEME-1.8.23/python/stempy/meme.py   STEME(Download)
        # parse output
        from Bio import Motif
        for motif in Motif.parse(open(os.path.join(self.options.output_dir, 'meme.txt')), "MEME"):
            for instance in motif.instances:
                # MEME parser seems to count from 1, not 0

src/s/e/seriesoftubes-0.9.6.9/scripts/analyze.py   seriesoftubes(Download)
    if not exists(foo):
        raise Usage(foo, "not found")
    motifs = Bio.Motif.parse(open(foo), motif_type)
    for i in xrange(motif_number):
        try: