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CoNekT/tests/utils.py
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| from utils.tau import tau | |
| from utils.entropy import entropy | |
| from utils.jaccard import jaccard | |
| from utils.sequence import translate | |
| from unittest import TestCase | |
| class UtilsTest(TestCase): | |
| def test_tau(self): | |
| self.assertEqual(tau([1, 0, 0, 0, 0, 0]), 1) | |
| self.assertEqual(tau([1, 1, 1, 1, 1, 1]), 0) | |
| self.assertEqual("%.2f" % tau([0, 8, 0, 0, 0, 2, 0, 2, 0, 0, 0, 0]), "0.95") # example from Yanai et al. 2005 | |
| def test_entropy(self): | |
| self.assertEqual(entropy([1, 0, 0, 0, 0, 0]), 0) | |
| def test_jaccard(self): | |
| self.assertEqual(jaccard('ab', 'bc'), 1/3) | |
| self.assertEqual(jaccard('ab', 'cd'), 0) | |
| self.assertEqual(jaccard('ab', 'ab'), 1) | |
| def test_sequence(self): | |
| sequence = "ATGTCAGAATTATTACAGTTGCCTCCAGGTTTCCGATTTCACCCTACCGATGAAGAGCTTGTCATGCACTATCTCTGCCGCAAATGTGCCTCTCAGTCCATCGCCGTTCCGATCATCGCTGAGATCGATCTCTACAAATACGATCCATGGGAGCTTCCTGGTTTAGCCTTGTATGGTGAGAAGGAATGGTACTTCTTCTCTCCCAGGGACAGAAAATATCCCAACGGTTCGCGTCCTAACCGGTCCGCTGGTTCTGGTTACTGGAAAGCTACCGGAGCTGATAAACCGATCGGACTACCTAAACCGGTCGGAATTAAGAAAGCTCTTGTTTTCTACGCCGGCAAAGCTCCAAAGGGAGAGAAAACCAATTGGATCATGCACGAGTACCGTCTCGCCGACGTTGACCGGTCCGTTCGCAAGAAGAAGAATAGTCTCAGGCTGGATGATTGGGTTCTCTGCCGGATTTACAACAAAAAAGGAGCTACCGAGAGGCGGGGACCACCGCCTCCGGTTGTTTACGGCGACGAAATCATGGAGGAGAAGCCGAAGGTGACGGAGATGGTTATGCCTCCGCCGCCGCAACAGACAAGTGAGTTCGCGTATTTCGACACGTCGGATTCGGTGCCGAAGCTGCATACTACGGATTCGAGTTGCTCGGAGCAGGTGGTGTCGCCGGAGTTCACGAGCGAGGTTCAGAGCGAGCCCAAGTGGAAAGATTGGTCGGCCGTAAGTAATGACAATAACAATACCCTTGATTTTGGGTTTAATTACATTGATGCCACCGTGGATAACGCGTTTGGAGGAGGAGGGAGTAGTAATCAGATGTTTCCGCTACAGGATATGTTCATGTACATGCAGAAGCCTTACTAG" | |
| translation = "MSELLQLPPGFRFHPTDEELVMHYLCRKCASQSIAVPIIAEIDLYKYDPWELPGLALYGEKEWYFFSPRDRKYPNGSRPNRSAGSGYWKATGADKPIGLPKPVGIKKALVFYAGKAPKGEKTNWIMHEYRLADVDRSVRKKKNSLRLDDWVLCRIYNKKGATERRGPPPPVVYGDEIMEEKPKVTEMVMPPPPQQTSEFAYFDTSDSVPKLHTTDSSCSEQVVSPEFTSEVQSEPKWKDWSAVSNDNNNTLDFGFNYIDATVDNAFGGGGSSNQMFPLQDMFMYMQKPY*" | |
| self.assertEqual(translate(sequence), translation) | |
| self.assertEqual(translate(sequence, trim=False), translation) | |
| self.assertNotEqual(translate("AAA" + sequence, trim=False), translation) | |
| self.assertEqual(translate("AAA" + sequence, trim=True), translation) | |
| self.assertNotEqual(translate(sequence+"AAA", return_on_stop=False), translation) | |
| self.assertEqual(translate(sequence+"AAA", return_on_stop=False), translation + "K") | |
| self.assertEqual(translate(sequence+"AAA", return_on_stop=True), translation) | |
| self.assertEqual(translate("ATGSEB"), "MX") |