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tests for sequence translation + caught bug !
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proost committed Sep 20, 2016
1 parent 8dabdf8 commit b7a5315
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Showing 2 changed files with 15 additions and 1 deletion.
14 changes: 14 additions & 0 deletions tests/utils.py
@@ -1,6 +1,7 @@
from utils.tau import tau
from utils.entropy import entropy
from utils.jaccard import jaccard
from utils.sequence import translate

from unittest import TestCase

Expand All @@ -18,3 +19,16 @@ 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")
2 changes: 1 addition & 1 deletion utils/sequence.py
Expand Up @@ -36,7 +36,7 @@ def translate(sequence, trim=True, return_on_stop=True):

if trim:
start = sequence.find('ATG')
trimmed_sequence[start:]
trimmed_sequence = trimmed_sequence[start:]

codons = [trimmed_sequence[i:i+3] for i in range(0, len(trimmed_sequence), 3)]

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