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#!/usr/bin/env python
# File created on 27 Sep 2011
from __future__ import division
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
__status__ = "Release"
from qiime.distance_matrix_from_mapping import distance_matrix
from numpy import array
from cogent.util.unit_test import TestCase, main
import StringIO
class FunctionTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
self.fasting_map = """#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Float_Col Description
#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 .1 Control_mouse__I.D._354
PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 .2 Control_mouse__I.D._355
PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 .3 Control_mouse__I.D._356
PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 .4 Control_mouse__I.D._481
PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 .5 Control_mouse__I.D._593
PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 .6 Fasting_mouse__I.D._607
PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 .7 Fasting_mouse__I.D._634
PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 .8 Fasting_mouse__I.D._635
PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 .9 Fasting_mouse__I.D._636"""
def test_distance_int(self):
""" distance calculations on ints should throw no errors"""
exp_out = "\tPC.481\tPC.607\tPC.634\tPC.635\tPC.593\tPC.636\tPC.355\tPC.354\tPC.356\nPC.481\t0.0\t798.0\t9802.0\t9802.0\t896.0\t9802.0\t9096.0\t9096.0\t9188.0\nPC.607\t798.0\t0.0\t9004.0\t9004.0\t98.0\t9004.0\t9894.0\t9894.0\t9986.0\nPC.634\t9802.0\t9004.0\t0.0\t0.0\t8906.0\t0.0\t18898.0\t18898.0\t18990.0\nPC.635\t9802.0\t9004.0\t0.0\t0.0\t8906.0\t0.0\t18898.0\t18898.0\t18990.0\nPC.593\t896.0\t98.0\t8906.0\t8906.0\t0.0\t8906.0\t9992.0\t9992.0\t10084.0\nPC.636\t9802.0\t9004.0\t0.0\t0.0\t8906.0\t0.0\t18898.0\t18898.0\t18990.0\nPC.355\t9096.0\t9894.0\t18898.0\t18898.0\t9992.0\t18898.0\t0.0\t0.0\t92.0\nPC.354\t9096.0\t9894.0\t18898.0\t18898.0\t9992.0\t18898.0\t0.0\t0.0\t92.0\nPC.356\t9188.0\t9986.0\t18990.0\t18990.0\t10084.0\t18990.0\t92.0\t92.0\t0.0"
res_out = distance_matrix(StringIO.StringIO(self.fasting_map), "DOB")
self.assertEqual(exp_out, res_out)
def test_distance_floats(self):
""" distance calculations on floats should throw no errors"""
# testing floats
exp_out = "\tPC.481\tPC.607\tPC.634\tPC.635\tPC.593\tPC.636\tPC.355\tPC.354\tPC.356\nPC.481\t0.0\t0.2\t0.3\t0.4\t0.1\t0.5\t0.2\t0.3\t0.1\nPC.607\t0.2\t0.0\t0.1\t0.2\t0.1\t0.3\t0.4\t0.5\t0.3\nPC.634\t0.3\t0.1\t0.0\t0.1\t0.2\t0.2\t0.5\t0.6\t0.4\nPC.635\t0.4\t0.2\t0.1\t0.0\t0.3\t0.1\t0.6\t0.7\t0.5\nPC.593\t0.1\t0.1\t0.2\t0.3\t0.0\t0.4\t0.3\t0.4\t0.2\nPC.636\t0.5\t0.3\t0.2\t0.1\t0.4\t0.0\t0.7\t0.8\t0.6\nPC.355\t0.2\t0.4\t0.5\t0.6\t0.3\t0.7\t0.0\t0.1\t0.1\nPC.354\t0.3\t0.5\t0.6\t0.7\t0.4\t0.8\t0.1\t0.0\t0.2\nPC.356\t0.1\t0.3\t0.4\t0.5\t0.2\t0.6\t0.1\t0.2\t0.0"
res_out = distance_matrix(StringIO.StringIO(self.fasting_map), "Float_Col")
self.assertEqual(exp_out, res_out)
#run tests if called from command line
if __name__ == '__main__':
main()
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