def test_motif_collection_to_yaml():
"""MotifCollection yaml export
Test MotifCollection's to_yaml method by loading a motifs definition
string, then converting it back to yaml via the to_yaml method,
then reloading the new yaml file and comparing with the original.
"""
mc1 = MotifCollection(yaml=MOTIF_TEST_YAML)
assert_instance_of(StringType, mc1.to_yaml())
mc2 = MotifCollection(yaml=mc1.to_yaml())
assert_equal(len(mc1), len(mc2))
for key in mc1:
assert(mc2.has_key(key))
assert_equal(mc1[key].id, mc2[key].id)
assert_equal(mc1[key].label, mc2[key].label)
assert_equal(len(mc1[key].sources), len(mc2[key].sources))
for val in mc1[key].sources:
assert(val in mc2[key].sources)
assert_equal(len(mc1[key].polymorphisms), len(mc2[key].polymorphisms))
for poly in mc1[key].polymorphisms:
assert poly in mc2[key].polymorphisms
def test_motif_collection_yaml_loading():
"""MotifCollection intialization with yaml data"""
mc = MotifCollection(yaml=MOTIF_TEST_YAML)
assert_equal(5, len(mc))
assert(mc.has_key(516))
assert(mc.has_key(1549))
assert(mc.has_key(1))
assert(mc.has_key(2582))
assert(mc.has_key(1033))
def test_motif_collection_motifs_loading():
"""MotifCollection intialization with Motif list"""
m1 = Motif(id=1, label="1")
m2 = Motif(id=2, label="2")
m3 = Motif(id=3, label="3")
mc = MotifCollection(motifs=[m1, m2, m3])
assert_equal(3, len(mc))
assert(mc.has_key(1))
assert(mc.has_key(2))
assert(mc.has_key(3))
assert_equal("1", mc[1].label)
assert_equal("2", mc[2].label)
assert_equal("3", mc[3].label)