def MOODS_search(seq, motif, thresholds=0):
"""an equivalent to Motif.search_pwm()"""
if not USE_MOODS:
raise RuntimeError("MOODS could not be imported")
sequence = seq
matrix_ = MOODS.transpose([map(lambda x: x[1], sorted(x.items())) for x in motif.log_odds()])
# Note: algorithm = 'lf' fails due to segmentation fault
results_per_matrix = MOODS.search(
sequence,
[matrix_],
thresholds,
bg=None,
algorithm="pla",
q=7,
absolute_threshold=True,
both_strands=True,
combine=True,
)
# format as Motif.search_pwm results
search_results = results_per_matrix[0]
# figure out direction of reverse results
# do we need to reverse it?
results_sorted_like_Bio_Motif = sorted(
search_results, key=operator.itemgetter(0), cmp=lambda x, y: cmp(abs(x), abs(y))
)
return results_sorted_like_Bio_Motif
