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#!/usr/bin/env python
# File created on 19 Jan 2010
from __future__ import division
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski"]
__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.parse import parse_distmat_to_dict, parse_mapping_file
from qiime.categorized_dist_scatterplot import get_avg_dists, get_sam_ids
import StringIO
class FunctionTests(TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_get_avg_dists(self):
"""get_avg_dists functions as expected """
dmtx_str = StringIO.StringIO("""\ts1\ts2\ts3
s1\t0\t.5\t.6
s2\t.5\t0\t.7
s3\t.6\t.7\t0.0
""")
distdict1 = parse_distmat_to_dict(dmtx_str)
distdict2 = {'s1':{'s2':.5,'s3':.6},'s2':{'s1':.5,'s3':.7},
's3':{'s2':.7,'s1':.6}}
state1_samids = ['s1','s2']
state2_samids = ['s3','s2']
# note s2 in both
exp_avgs = [.55, .7]
obs_avgs = get_avg_dists(state1_samids,state2_samids,distdict1)
self.assertFloatEqual(exp_avgs, obs_avgs)
def test_get_sam_ids(self):
"""set of sample ids in get_sam_ids should be correct"""
map_file = StringIO.StringIO("""#SampleID Country AgeYears Family AgeCat
h208A.1 Malawi 0.032854209 h208 Child
h301A.1 Malawi 0.05 h301 Child
h301B.1 Malawi 0.05 h301 Child
USinfTw20.1 USA 0.083333333 USinfTw20 Child
USinfTw20.2 USA 0.083333333 USinfTw20 Child
USinfTw1.1 USA 0.083333333 USinfTw1 Child
h10M Malawi 26 h10 Adult
h68M Malawi 26 h68 Adult
TS25 USA 26 USts9 Adult
TS26 USA 26 USts9 Adult""")
map_data, map_header, comments = parse_mapping_file(map_file)
colorby = 'Country'
cat = 'USA'
primary_state = 'AgeCat:Child'
ids1, ids2 = get_sam_ids(map_data, map_header, colorby, cat,
primary_state, secondary_state=None)
self.assertEqual(set(ids1),
set(['USinfTw20.1','USinfTw20.2','USinfTw1.1']))
self.assertEqual(set(ids2), set(['TS25','TS26']))
if __name__ == "__main__":
main()
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