test_barcode.py

#!/usr/bin/env python

__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"  # consider project name
# remember to add yourself if you make changes
__credits__ = ["Justin Kuczynski", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"

from unittest 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()