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#!/usr/bin/env python
# test_hamming.py
"""
Tests for standalone Hamming decoding function
Author: Micah Hamady (hamady@colorado.edu)
"""
__author__ = "Micah Hamady"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Micah Hamady", "Rob Knight"] #remember to add yourself
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from qiime.hamming import decode_barcode_8
class GeneralSetUp(TestCase):
def setUp(self):
"""General Setup"""
# valid code words
self.valid_bc_1 = "AACCATGC"
self.valid_bc_2 = "TCGTAGCA"
self.valid_bc_3 = "ACACCTCT"
self.valid_bc_4 = "CTTCCTAG"
self.valid_bc_5 = "GGTAGCTT"
# single error reference
self.single_error_ref = "AACCATGC"
# A->C
self.single_error_1 = "ACCCATGC"
# A->G
self.single_error_2 = "AACCGTGC"
# C->A
self.single_error_3 = "AAACATGC"
# C->T
self.single_error_4 = "AACCATGT"
# T->C
self.single_error_5 = "AACCACGC"
# T->G
self.single_error_6 = "AACCAGGC"
# G->T
self.single_error_7 = "AACCATTC"
# G->A
self.single_error_8 = "AACCATAC"
# double error reference
self.double_error_ref = "AACCATGC"
# A->T
self.double_error_1 = "ATCCATGC"
# T->A
self.double_error_2 = "AACCAAGC"
# C->G
self.double_error_3 = "AACGATGC"
#aG->C
self.double_error_4 = "AACCATCC"
class StandaloneHammingTests(GeneralSetUp):
"""Tests for the standalone_hamming functions"""
def test_decode_barcode_8_ok(self):
""" Should decode valid codewords w/o error """
self.assertEqual(decode_barcode_8(self.valid_bc_1), \
(self.valid_bc_1, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_2), \
(self.valid_bc_2, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_3), \
(self.valid_bc_3, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_4), \
(self.valid_bc_4, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_5), \
(self.valid_bc_5, 0))
def test_decode_barcode_8_one_error(self):
""" Should correct single bit errors w/o error """
self.assertEqual(decode_barcode_8(self.single_error_1), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_2), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_3), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_4), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_5), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_6), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_7), \
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_8), \
(self.single_error_ref, 0.5))
def test_decode_barcode_8_two_error(self):
""" Should raise error when double error detected """
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
if __name__ == '__main__':
main()
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