def testDistanceMatrix(self):
"""
It must be possible to produce a distance matrix for a feature.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 6\n'
'name3, 7, 8\n')
m = Matrix(csv)
self.assertEqual(
[[0.0, -2.0, -4.0], [2.0, 0.0, -2.0], [4.0, 2.0, 0.0]],
m.distanceMatrix('A', logged=False))
def testUpperDiagonal(self):
"""
It must be possible to produce the upper diagonal of a distance matrix
for a feature.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 6\n'
'name3, 7, 8\n')
m = Matrix(csv)
self.assertEqual([-2.0, -4.0, -2.0], m.upperDiagonal('A',
logged=False))
def testUpperDiagonalAsXML(self):
"""
It must be possible to produce XML for the upper diagonal of a
distance matrix for a feature.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 6\n'
'name3, 7, 8\n')
m = Matrix(csv)
element = m.upperDiagonalAsXML('A', logged=False)
self.assertEqual(('<xxx><value>-2.0</value><value>-4.0</value>'
'<value>-2.0</value></xxx>'),
tostring(element, encoding=ENCODING))
def testTaxaNames(self):
"""
The taxa names must be correctly extracted.
"""
csv = StringIO('Ignored, A, B\n' 'name1, 3, 4\n' 'name2, 5, 6\n')
m = Matrix(csv)
self.assertEqual(['name1', 'name2'], list(m.taxa))
def testFeatureNames(self):
"""
The feature names must be correctly extracted.
"""
csv = StringIO('Ignored, A, B\n' 'name, 3, 4\n')
m = Matrix(csv)
self.assertEqual(['A', 'B'], list(m.features))
def testDistanceMatrixLoggedByDefault(self):
"""
The distance matrices produced for a feature must have their values
logged by default.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 6\n'
'name3, 7, 8\n')
m = Matrix(csv)
L3 = log10(3.0)
L5 = log10(5.0)
L7 = log10(7.0)
self.assertEqual([[0.0, L3 - L5, L3 - L7], [L5 - L3, 0.0, L5 - L7],
[L7 - L3, L7 - L5, 0.0]], m.distanceMatrix('A'))
def testFeatureValues(self):
"""
The feature values must be correctly extracted.
"""
csv = StringIO('Ignored, A, B\n' 'name1, 3, 4\n' 'name2, 5, 6\n')
m = Matrix(csv)
self.assertEqual([3.0, 5.0], m.features['A'])
self.assertEqual([4.0, 6.0], m.features['B'])
def testDistanceMatrixLogged(self):
"""
It must be possible to produce a distance matrix for a feature
whose values have been logged.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 6\n'
'name3, 7, 8\n')
m = Matrix(csv)
L3 = log10(3.0)
L5 = log10(5.0)
L7 = log10(7.0)
self.assertEqual([[0.0, L3 - L5, L3 - L7], [L5 - L3, 0.0, L5 - L7],
[L7 - L3, L7 - L5, 0.0]],
m.distanceMatrix('A', logged=True))
def testTaxaValues(self):
"""
The taxa values must be correctly extracted.
"""
csv = StringIO('Ignored, A, B\n' 'name1, 3, 4\n' 'name2, 5, 6\n')
m = Matrix(csv)
self.assertEqual([3.0, 4.0], m.taxa['name1'])
self.assertEqual([5.0, 6.0], m.taxa['name2'])
def testUpperDiagonalForUnknownFeature(self):
"""
A KeyError must be raised if an attempt is made to get the upper
diagonal for an unknown feature.
"""
csv = StringIO('Ignored, A, B, C\n'
'name1, 1, 2, 3\n'
'name2, 4, 5, 6\n')
m = Matrix(csv)
error = "^'XXX'$"
assertRaisesRegex(self, KeyError, error, m.upperDiagonal, 'XXX')
def testDistanceMatrixForUnknownFeature(self):
"""
A KeyError must be raised if an attempt is made to get a distance
matrix for an unknown feature.
"""
csv = StringIO('Ignored, A, B, C\n'
'name1, 1, 2, 3\n'
'name2, 4, 5, 6\n')
m = Matrix(csv)
error = "^'XXX'$"
assertRaisesRegex(self, KeyError, error, m.distanceMatrix, 'XXX')
def testAllfeaturesAsXML(self):
"""
It must be possible to produce XML for the upper diagonal of the
distance matrices for all features.
"""
csv = StringIO('Ignored, A, B\n'
'name1, 3, 4\n'
'name2, 5, 7\n'
'name3, 7, 9\n')
m = Matrix(csv)
element = m.allFeaturesAsXML(logged=False)
self.assertEqual(
('<xxx>'
'<!--A-->'
'<feature>'
'<value>-2.0</value><value>-4.0</value><value>-2.0</value>'
'</feature>'
'<!--B-->'
'<feature>'
'<value>-3.0</value><value>-5.0</value><value>-2.0</value>'
'</feature>'
'</xxx>'), tostring(element, encoding=ENCODING))
#!/usr/bin/env python
import argparse
import sys
from xml.etree.ElementTree import ElementTree
from cbeast.matrix import Matrix
parser = argparse.ArgumentParser(description='Convert CSV to XML for BEAST')
parser.add_argument(
'--fragment',
action='store_true',
default=False,
help='If specified, output only an XML fragment (for pasting).')
args = parser.parse_args()
ElementTree(Matrix(sys.stdin).allFeaturesAsXML()).write(
sys.stdout, encoding='unicode', xml_declaration=(not args.fragment))