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#!/usr/bin/env python
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Justin Kuczynski", "Rob Knight"] #remember to add yourself if you make changes
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
import qiime.barcode as barcode
class BarcodeTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""Set up shared variables"""
def test_correct_barcode(self):
""" correct_barcode should correctly assign barcode to 2nd possibility,
2 errors
"""
original = 'ATTTTTTTTTCG'
recieved = 'ATTTTTTTTTTT'
possibilities = ['TGTATTCGTGTA','ATTTTTTTTTCG','TGTAGGCGTGTA',
'TGTAGAAGTGTA','TGTAGGCGTATA','TGTAAAAAAAAA']
decoded, num_errors = barcode.correct_barcode(recieved, possibilities)
self.assertEqual(decoded, original)
self.assertEqual(num_errors, 2)
def test_correct_barcode_bitwise(self):
""" correct_barcode should correctly assign barcode to 2nd possibility,
2 base errors,
3 bit errors with this nt_to_bits
"""
nt_to_bits = { "A":"11", "C":"00", "T":"10", "G":"01"}
original = 'ATTTTTTTTTCG'
recieved = 'ATTTTTTTTTTT'
possibilities = ['TGTATTCGTGTA','ATTTTTTTTTCG','TGTAGGCGTGTA',
'TGTAGAAGTGTA','TGTAGGCGTATA','TGTAAAAAAAAA']
decoded, num_errors = barcode.correct_barcode_bitwise(\
recieved, possibilities, nt_to_bits)
self.assertEqual(decoded, original)
self.assertEqual(num_errors, 3)
def test_correct_barcode_bitwise_tie(self):
""" correct_barcode should not assign barcode to to a tie situation
"""
nt_to_bits = { "A":"11", "C":"00", "T":"10", "G":"01"}
#~ original = 'ATTTTTTTTTCG' #doesn't matter, last entry is just
# as close to recieved as original is
recieved = 'ATTTTTTTTTTT'
possibilities = ['TGTATTCGTGTA','ATTTTTTTTTCG','TGTAGGCGTGTA',
'TGTAGAAGTGTA','TGTAGGCGTATA','TGTAAAAAAAAA', 'ATTTTTTTTAAA']
decoded, num_errors = barcode.correct_barcode_bitwise(\
recieved, possibilities, nt_to_bits)
self.assertEqual(decoded, None)
self.assertEqual(num_errors, 3)
if __name__ == '__main__':
main()
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