def test_distances_individuals_missing_data(self):
#Diploid
ms1 = eden.MicrosatelliteData(self.data2)
dm1 = ms1.getDistanceMatrix(distance="lm")
assert dm1[
0,
1] == 2.0, "Diploid data: Error calculating the linear manhattan distance."
dm2 = ms1.getDistanceMatrix(distance="ap")
assert dm2[
0,
1] == 2.0, "Diploid data: Error calculating the allele parsimony distance."
#Haploid
ms2 = eden.MicrosatelliteDataHaploid(self.data2)
dm3 = ms2.getDistanceMatrix(distance="lm")
assert dm3[0, 1] == (
3 * 1.0 + 29.0
) / 4.0, "Haploid data: Error calculating the linear manhattan distance."
dm4 = ms2.getDistanceMatrix(distance="ap")
assert dm4[
0,
1] == 1.0, "Haploid data: Error calculating the allele parsimony distance."
#Haploid, large amounts of missing data
ms3 = eden.MicrosatelliteDataHaploid(self.data3)
dm5 = ms3.getDistanceMatrix(distance="lm")
assert dm5[0, 1] == 0.0, "Missing data: Error."
assert dm5[
0,
2] == -1, "Missing data: No matchind data fields should lead to -1 distance."
def test_distances_allele_freqs(self):
ms1 = eden.MicrosatelliteDataHaploid(self.data_nonnumeric2)
af1 = eden.AlleleFrequencyTable()
try:
af1.init_msData(ms1, [[0, 1], [2, 3]])
except eden.EDENException, e:
assert "input data has" in str(e)
def test_distances_populations_missing_data(self):
#Diploid
ms1 = eden.MicrosatelliteData(self.data2)
dm1 = ms1.getGroupwiseDistanceMatrix(groups=[[0], [1]],
distance="goldstein_d1")
assert dm1[0, 1] == (
0.5 * 1 + 0.25 * (1 + 21 * 21 + 19 * 19 + 1) + 0.5 * (29 * 29 + 1)
) / 3.0, "Diploid data: Error calculating the goldstein D1 distance."
dm3 = ms1.getGroupwiseDistanceMatrix(groups=[[0], [1]],
distance="goldstein")
assert dm3[0, 1] == (
((100 + 101) / 2. - (101) / 1.)**2 +
((200 + 220) / 2. - (201 + 221) / 2.)**2 + ((330) / 1. -
(301 + 331) / 2.)**
2) / 3., "Diploid data: Error calculating the goldstein distance."
#Haploid
ms2 = eden.MicrosatelliteDataHaploid(self.data2)
dm2 = ms2.getGroupwiseDistanceMatrix(groups=[[0], [1]],
distance="goldstein_d1")
assert dm2[0, 1] == (
1 + 1 + 1 + 29 * 29
) / 4.0, "Haploid data: Error calculating the goldstein D1 distance."
dm4 = ms2.getGroupwiseDistanceMatrix(groups=[[0], [1]],
distance="goldstein")
assert dm4[0, 1] == (
1 + 1 + 1 + 29 * 29
) / 4.0, "Haploid data: Error calculating the goldstein distance."
def test_distances_individuals(self):
#Diploid
ms1 = eden.MicrosatelliteData(self.data1)
dm1 = ms1.getDistanceMatrix(distance="lm")
assert dm1[
0,
1] == 2.0, "Diploid data: Error calculating the linear manhattan distance."
dm2 = ms1.getDistanceMatrix(distance="ap")
assert dm2[0, 1] == (
1.0 + 2.0 + 2.0
) / 3.0, "Diploid data: Error calculating the allele parsimony distance."
#Haploid
ms2 = eden.MicrosatelliteDataHaploid(self.data1)
dm3 = ms2.getDistanceMatrix(distance="lm")
assert dm3[0, 1] == (
4 * 1.0 + 29.0 + 31.0
) / 6.0, "Haploid data: Error calculating the linear manhattan distance."
dm4 = ms2.getDistanceMatrix(distance="ap")
assert dm4[
0,
1] == 1.0, "Haploid data: Error calculating the allele parsimony distance."
def __init__(self,
data,
groups=True,
ind_distance="lm",
group_distance="goldstein_d1",
ploidity=2):
self.tests = self.tests_slow + self.tests_fast
if isinstance(data, str) or isinstance(data, unicode):
data = open(data, 'r')
self.ind_distance = ind_distance
self.group_distance = group_distance
if groups:
locs, names, data = splitMSFile(data)
self.data = data
self.locs = locs
self.names = names
self.pops, names = eden.getGoldsteinLists(locs)
else:
names, data = splitMSFile(data, locations=False)
self.data = data
self.names = names
if ploidity == 2:
self.ms = eden.MicrosatelliteData(self.data)
elif ploidity == 1:
self.ms = eden.MicrosatelliteDataHaploid(self.data)
else:
raise Exception("invalid ploidity")
self.ms_noclones = self.ms.getUniqueSubset()
if groups:
self.dm_groups = self.get_dm_groups()
self.thnet_groups = self.auto_threshold_groups()
self.dm_ind = self.get_dm_ind()
self.thnet_ind = self.auto_threshold_ind()
def test_distances_abundances(self):
data1 = eden.MicrosatelliteDataHaploid(self.abundance_data1)
dm1 = data1.getDistanceMatrix(distance="czekanowski")
assert dm1[0, 1] == 1 - 2 / 3.0 and dm1[0, 2] == 1 - 0.5 and dm1[
1, 2] == 1 - 0.4
def test_distances_individuals_nonnumeric(self):
ms1 = eden.MicrosatelliteDataHaploid(self.data_nonnumeric1)
dm1 = ms1.getDistanceMatrix(distance="ap")
assert dm1[
0,
1] == 1. - 3. / 5., "Error calculating the allele parsimony distance for non-numeric data."