def testNumberDef(self):
NumDef = Enumeration("NumDef",
(("neg", None, None, -2),
("zero", None, None, 0),
("pos", None, None, 2),
("big", None, None, 3)))
values = [(str(v), int(v)) for v in NumDef.values]
self.assertEqual(values, [('neg', -2), ('zero', 0), ('pos', 2), ('big', 3)])
self.assertEqual(NumDef.getByNumValue(2), NumDef.pos)
def testBitSetValues(self):
Stat = Enumeration("Stat",
["okay",
("notConserved","notConserved", ("no_alignment",)),
"bad_3_splice", "bad_5_splice"],
bitSetValues=True)
self.assertEqual(Stat.okay, 1)
self.assertEqual(Stat.notConserved, 2)
self.assertEqual(Stat.bad_5_splice, 8)
self.assertEqual(int(Stat.bad_5_splice), 8)
self.assertEqual(Stat.maxNumValue, 8)
vals = Stat.getValues(9)
self.assertEqual(len(vals), 2)
self.assertTrue(vals[0] is Stat.okay)
self.assertTrue(vals[1] is Stat.bad_5_splice)
def testAliases(self):
Name = Enumeration("Name", ["Fred", ("Rick", "Richard", ("Dick", "HeyYou")), ("Bill", "Willian")])
self.assertEqual(Name.lookup("Richard"), Name.Rick)
self.assertTrue(Name.lookup("Richard") is Name.Rick)
self.assertEqual(Name.lookup("Dick"), Name.Rick)
self.assertTrue(Name.lookup("Dick") is Name.Rick)
self.assertTrue(Name.lookup("Rick") == Name.Rick)
self.assertTrue(Name.lookup("HeyYou") == Name.Rick)
self.assertTrue(Name.lookup("Fred") == Name.Fred)
self.assertTrue(Name.lookup("Fred") is Name.Fred)
self.assertTrue(str(Name.Rick) == "Richard")
# definitions, then create the enumerations from that.
# FIXME: sql select stuff is a bit hacky
BioType = Enumeration(
"BioType",
("IG_C_gene", "IG_D_gene", "IG_J_gene", "IG_V_gene", "IG_LV_gene",
"IG_C_pseudogene", "IG_D_pseudogene", "IG_pseudogene", "IG_J_pseudogene",
"IG_V_pseudogene", "TR_gene", "TR_C_gene", "TR_D_gene", "TR_J_gene",
"TR_V_gene", "ambiguous_orf", "antisense", "lincRNA", "Mt_rRNA",
"Mt_tRNA", "Mt_tRNA_pseudogene", "TEC", "TR_pseudogene",
"TR_J_pseudogene", "TR_V_pseudogene", "miRNA", "miRNA_pseudogene",
"misc_RNA", "ncrna_host", "misc_RNA_pseudogene", "non_coding",
"nonsense_mediated_decay", "polymorphic_pseudogene",
"processed_pseudogene", "processed_transcript", "protein_coding",
"pseudogene", "rRNA", "rRNA_pseudogene", "retained_intron",
"retrotransposed", "scRNA", "scRNA_pseudogene", "snRNA",
"snRNA_pseudogene", "snoRNA", "snoRNA_pseudogene", "tRNA_pseudogene",
"transcribed_processed_pseudogene", "transcribed_unprocessed_pseudogene",
"unitary_pseudogene", "transcribed_unitary_pseudogene",
"unprocessed_pseudogene",
("overlapping_ncrna_3prime", "3prime_overlapping_ncrna"),
("overlapping_ncRNA_3prime",
"3prime_overlapping_ncRNA"), "disrupted_domain", "sense_intronic",
"sense_overlapping", "non_stop_decay", "translated_processed_pseudogene",
"translated_unprocessed_pseudogene", "known_ncrna", "macro_lncRNA",
"ribozyme", "scaRNA", "sRNA", "vaultRNA", "bidirectional_promoter_lncrna",
"bidirectional_promoter_lncRNA"))
BioTag = Enumeration(
"BioTag",
(
"2way_pseudo_cons",
