def setUp(self):
self.alphabet = IUPAC.ambiguous_dna
self.test_file = os.path.join("NeuralNetwork", "patternio.txt")
#Remove any existing copy of the output file,
if os.path.isfile(self.test_file):
os.remove(self.test_file)
self.pattern_io = Pattern.PatternIO(self.alphabet)
def test_easy_from_motifs(self):
"""Generating schema from a simple list of motifs."""
motif_bank = Pattern.PatternRepository(self.motifs)
schema_bank = self.factory.from_motifs(motif_bank, .5, 2)
if VERBOSE:
print("\nSchemas:")
for schema in schema_bank.get_all():
print("%s: %s" % (schema, schema_bank.count(schema)))
def setUp(self):
self.motifs = {"GATC" : 30,
"GGGG" : 10,
"GTAG" : 0,
"AAAA" : -10,
"ATAT" : -20}
self.repository = Pattern.PatternRepository(self.motifs)
def test_easy_from_motifs(self):
"""Generating schema from a simple list of motifs.
"""
motifs = {"GATCGAA": 20, "GATCGAT": 15, "GATTGAC": 25, "TTTTTTT": 10}
motif_bank = Pattern.PatternRepository(motifs)
schema_bank = self.factory.from_motifs(motif_bank, .5, 2)
if VERBOSE:
print "\nSchemas:"
for schema in schema_bank.get_all():
print "%s: %s" % (schema, schema_bank.count(schema))
def test_no_motifs(self):
"""Test generating schema when no motif given."""
motif_bank = Pattern.PatternRepository({})
with self.assertRaises(ValueError):
self.factory.from_motifs(motif_bank, .5, 2)