def test_motif_scoring(self):
meme_suite = meme.MemeSuite430({'MEME': {'max_width': 24, 'background_order': 3,
'use_revcomp': 'True', 'arg_mod': 'zoops'}})
sequence_filters = [
motif.unique_filter,
motif.get_remove_low_complexity_filter(meme_suite),
motif.get_remove_atgs_filter(self.search_distances['upstream'])]
motif_scoring = motif.MemeScoringFunction(
self.organism, self.membership, self.ratio_matrix,
config_params=self.config_params)
motscores = motif_scoring.compute(self.iteration_result).sorted_by_row_name()
motscores.fix_extreme_values()
ref_motscores = read_matrix('testdata/ref_motscores.tsv')
self.assertTrue(check_matrix_values(motscores, ref_motscores))
def test_motif_scoring(self):
"""tests the motif scoring in integration"""
search_distances = {'upstream': (-20, 150)}
scan_distances = {'upstream': (-30, 250)}
matrix_factory = dm.DataMatrixFactory(
[dm.nochange_filter, dm.center_scale_filter])
infile = util.read_dfile('example_data/hal/halo_ratios5.tsv',
has_header=True,
quote='\"')
ratio_matrix = matrix_factory.create_from(infile)
organism = testutil.make_halo(search_distances, scan_distances,
ratio_matrix)
membership = FakeMembership()
config_params = {
'memb.min_cluster_rows_allowed': 3,
'memb.max_cluster_rows_allowed': 70,
'multiprocessing': False,
'num_clusters': 1,
'output_dir': 'out',
'debug': {},
'search_distances': {
'upstream': (-20, 150)
},
'num_iterations': 2000,
'MEME': {
'schedule': lambda i: True,
'version': '4.3.0',
'global_background': False,
'arg_mod': 'zoops',
'nmotifs_rvec':
'c(rep(1, num_iterations/3), rep(2, num_iterations/3))',
'use_revcomp': 'True',
'max_width': 24,
'background_order': 3
},
'Motifs': {
'schedule': lambda i: True,
'scaling': ('scaling_const', 1.0)
}
}
func = motif.MemeScoringFunction(organism,
membership,
ratio_matrix,
config_params=config_params)
iteration_result = {'iteration': 100}
matrix = func.compute(iteration_result)