def test_species_with_three_words_name(self):
"""should correctly parse a db name that contains a three words species name"""
n = EnsemblDbName("mustela_putorius_furo_core_70_1")
self.assertEqual(n.prefix, "mustela_putorius_furo")
self.assertEqual(n.type, "core")
self.assertEqual(n.build, "1")
self.assertEqual(n.species, "Mustela putorius furo")
n = EnsemblDbName("canis_lupus_familiaris_core_102_31")
self.assertEqual(n.species, "Canis lupus familiaris")
def test_ensemblgenomes_names(self):
"""correctly handle the ensemblgenomes naming system"""
n = EnsemblDbName("aedes_aegypti_core_5_58_1e")
self.assertEqual(n.prefix, "aedes_aegypti")
self.assertEqual(n.type, "core")
self.assertEqual(n.release, "5")
self.assertEqual(n.general_release, "58")
self.assertEqual(n.build, "1e")
n = EnsemblDbName("ensembl_compara_metazoa_6_59")
self.assertEqual(n.release, "6")
self.assertEqual(n.general_release, "59")
self.assertEqual(n.type, "compara")
def reduce_dirnames(dirnames, species_dbs, verbose=False, debug=False):
"""returns EnsemblNames corresponding to species db's and sort by type
sort order put's core db's first, compara and variation last"""
if debug:
pprint(dirnames)
db_names = []
for record in dirnames:
record = record.strip()
if not record or record.endswith(".gz"):
continue
record = record.split()[-1]
if not record[0].isalpha():
continue
try:
name = EnsemblDbName(record)
except (TypeError, RuntimeError):
# a non-species
if debug:
print(record)
continue
if name.species in species_dbs:
if name.type not in species_dbs[name.species] and species_dbs[
name.species]:
if debug or verbose:
print("Skipping", name)
continue
db_names.append(name)
elif name.type == "compara" and "compara" in species_dbs:
db_names.append(name)
db_names = _sort_dbs(db_names)
return db_names
def test_name_without_build(self):
"""should correctly handle a db name without a build"""
n = EnsemblDbName("pongo_pygmaeus_core_49_1")
self.assertEqual(n.prefix, "pongo_pygmaeus")
self.assertEqual(n.type, "core")
self.assertEqual(n.build, "1")
def test_cmp_name(self):
"""should validly compare names by attributes"""
n1 = EnsemblDbName("homo_sapiens_core_46_36h")
n2 = EnsemblDbName("homo_sapiens_core_46_36h")
self.assertEqual(n1, n2)
def test_species_with_three_words_name(self):
"""should correctly parse a db name that contains a three words species name"""
n = EnsemblDbName("mustela_putorius_furo_core_70_1")
self.assertEqual(n.prefix, "mustela_putorius_furo")
self.assertEqual(n.type, "core")
self.assertEqual(n.build, "1")