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 __setup_meme_suite(self, config_params):
background_file = None
bgmodel = None
meme_version = config_params['MEME']['version']
search_distance = config_params['search_distances'][self.seqtype]
if config_params['MEME']['global_background'] == 'True':
background_file, bgmodel = meme.global_background_file(
self.organism,
self.ratios.row_names,
self.seqtype,
bgorder=int(self.config_params['MEME']['background_order']))
# store background in results database
conn = sqlite3.connect(config_params['out_database'],
15,
isolation_level='DEFERRED')
for order in bgmodel:
for subseq, pvalue in order.items():
conn.execute(
'insert into global_background (subsequence, pvalue) values (?,?)',
(subseq, pvalue))
conn.commit()
conn.close()
if meme_version == '4.3.0':
self.meme_suite = meme.MemeSuite430(
self.config_params,
background_file=background_file,
bgmodel=bgmodel)
elif meme_version and (meme_version.startswith('4.8')
or meme_version.startswith('4.9')
or meme_version.startswith('4.10')
or meme_version.startswith('4.11')):
self.meme_suite = meme.MemeSuite481(
self.config_params,
background_file=background_file,
bgmodel=bgmodel)
else:
logging.error("MEME version %s currently not supported !",
meme_version)
raise Exception("unsupported MEME version: '%s'" % meme_version)
self.__sequence_filters = [
unique_filter,
get_remove_low_complexity_filter(self.meme_suite),
get_remove_atgs_filter(search_distance)
]
def __setup_meme_suite(self, config_params):
background_file = None
bgmodel = None
meme_version = config_params['MEME']['version']
search_distance = config_params['search_distances'][self.seqtype]
if config_params['MEME']['global_background'] == 'True':
background_file, bgmodel = meme.global_background_file(
self.organism,
self.ratios.row_names,
self.seqtype,
bgorder=int(self.config_params['MEME']['background_order']))
# store background in results database
session = cm2db.make_session_from_config(config_params)
for order in bgmodel:
session.add_all([
cm2db.GlobalBackground(subsequence=subseq, pvalue=pvalue)
for subseq, pvalue in order.items()
])
session.commit()
session.close()
if meme_version == '4.3.0':
self.meme_suite = meme.MemeSuite430(
self.config_params,
background_file=background_file,
bgmodel=bgmodel)
elif meme_version and (meme_version.startswith('4.8')
or meme_version.startswith('4.9')
or meme_version.startswith('4.10')
or meme_version.startswith('4.11')):
self.meme_suite = meme.MemeSuite481(
self.config_params,
background_file=background_file,
bgmodel=bgmodel)
else:
logging.error("MEME version %s currently not supported !",
meme_version)
raise Exception("unsupported MEME version: '%s'" % meme_version)
self.__sequence_filters = [
unique_filter,
get_remove_low_complexity_filter(self.meme_suite),
get_remove_atgs_filter(search_distance)
]
def test_meme_simple(self):
"""simplest of all: just run meme and parse the output, just tests
if there will be appropriate output for the input"""
meme_suite = meme.MemeSuite430({
'MEME': {
'max_width': 24,
'background_order': 3,
'use_revcomp': 'True',
'arg_mod': 'zoops'
}
})
motif_infos, out = meme_suite.meme('testdata/meme_input1.fasta',
'testdata/meme1.bg',
num_motifs=1)
self.assertEquals(1, len(motif_infos))
self.assertEquals(24, motif_infos[0].width)
self.assertEquals(3, motif_infos[0].num_sites)
self.assertEquals(79, motif_infos[0].llr)
self.assertAlmostEquals(1700, motif_infos[0].evalue)