diff --git a/solventmapcreator/io/linkagewriter.py b/solventmapcreator/io/linkagewriter.py
index f9d399b287bfea30ed3e79398fbf3c7fb8423621..0555fd8fa12613ca26f2e55bb9300a4c5ad4df10 100644
--- a/solventmapcreator/io/linkagewriter.py
+++ b/solventmapcreator/io/linkagewriter.py
@@ -7,9 +7,9 @@ Script for writing out the linkage matrix, as well as the statistics.
"""
import logging
+import scipy.spatial.distance as scidist
import csv
-
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
@@ -31,4 +31,56 @@ def create_linkage_file_line(linkage_matrix_row):
return ["{:.0f}".format(linkage_matrix_row[0]),
"{:.0f}".format(linkage_matrix_row[1]),
"{:.7f}".format(linkage_matrix_row[2]),
- "{:.0f}".format(linkage_matrix_row[3])]
\ No newline at end of file
+ "{:.0f}".format(linkage_matrix_row[3])]
+
+def write_cophenetic_and_inconsistency(cophenetic_coefficient,
+ cophenetic_distances,
+ inconsistency_matrix, filename):
+ """This writes out the cophenetic and inconsistency information.
+ """
+ cophenetic_lines = create_cophenetic_lines(cophenetic_coefficient, cophenetic_distances)
+ inconsistency_lines = create_inconsistency_lines(inconsistency_matrix)
+ with open(filename, 'w') as outfile:
+ csv_writer = csv.writer(outfile, delimiter='\t',
+ quoting=csv.QUOTE_NONE)
+ csv_writer.writerows(cophenetic_lines)
+ csv_writer.writerows(inconsistency_lines)
+ return 0
+
+
+def create_cophenetic_lines(cophenetic_coefficient, cophenetic_distances):
+ """This creates a list of lists containing the cophenetic coefficient and
+ the cophenetic distances.
+ """
+ cophenetic_information = []
+ cophenetic_coefficient_line = ["Cophenetic coefficient", "{:.7f}".format(cophenetic_coefficient)]
+ cophenetic_information.append(cophenetic_coefficient_line)
+ cophenetic_information.append(["Cophenetic Distance Matrix"])
+ square_form_cophenetic_dists = scidist.squareform(cophenetic_distances)
+ for i in range(square_form_cophenetic_dists.shape[0]):
+ cophenetic_information.append(create_cophenetic_distance_line(square_form_cophenetic_dists[i]))
+ return cophenetic_information
+
+def create_cophenetic_distance_line(cophenetic_distance_line):
+ """This creastes a line from the symmetric square distance matrix.
+ """
+ return ["{:.7f}".format(cophenetic_distance_line[i]) for i in range(cophenetic_distance_line.shape[0])]
+
+def create_inconsistency_lines(inconsistency_matrix):
+ """This creates a list of lists containing the inconsistency matrix
+ information ready for writing to file.
+ """
+ inconsistency_information = []
+ header_line = ["Mean Heights of links", "SD for links", "Number of links", "Inconsistency coefficient"]
+ inconsistency_information.append(header_line)
+ for i in range(inconsistency_matrix.shape[0]):
+ inconsistency_information.append(create_inconsistency_line(inconsistency_matrix[i]))
+ return inconsistency_information
+
+def create_inconsistency_line(inconsistency_matrix_line):
+ """This formats the information in the inconsistency line for writing out.
+ """
+ return ["{:.7f}".format(inconsistency_matrix_line[0]),
+ "{:.7f}".format(inconsistency_matrix_line[1]),
+ "{:.1f}".format(inconsistency_matrix_line[2]),
+ "{:.7f}".format(inconsistency_matrix_line[3])]
diff --git a/solventmapcreator/test/iotest/linkagewritertest.py b/solventmapcreator/test/iotest/linkagewritertest.py
index 7db36197d6a06d527fd41bf6a4f09553fc6b04c4..ae466413036925c4d1dac70c6f65a94d5d4e2b31 100644
--- a/solventmapcreator/test/iotest/linkagewritertest.py
+++ b/solventmapcreator/test/iotest/linkagewritertest.py
@@ -27,12 +27,22 @@ class LinkageWriterTestCase(unittest.TestCase):
[2., 3., 28., 2.],
[6., 7., 33., 5.]])
self.expected_filename = "resources/expectedlinkagematrix.csv"
+ self.inconsistency_matrix = np.array([[17., 0., 1., 0.],
+ [19.5, 3.535534, 2., 0.707107],
+ [28., 0., 1., 0.],
+ [27.666667,5.507571, 3., 0.968364]])
+ self.cophenetic_coefficient = 0.73020316123580109
+ self.cophenetic_distance_matrix = np.array([17., 33., 33., 22., 33.,
+ 33., 22., 28., 33., 33.])
+ self.expected_cop_filename = "resources/expectedcopfile.csv"
def tearDown(self):
"""Clean up after tests.
"""
del self.linkage_matrix
if os.path.isfile("linkagematrix.csv"):
os.remove("linkagematrix.csv")
+ if os.path.isfile("coph_incons.csv"):
+ os.remove("coph_incons.csv")
def test_write_linkage_matrix(self):
"""Test to see if expected file is produced.
"""
@@ -51,3 +61,53 @@ class LinkageWriterTestCase(unittest.TestCase):
expected_list = ['0', '1', '17.0000000', '2']
actual_list = linkagewriter.create_linkage_file_line(self.linkage_matrix[0])
self.assertListEqual(expected_list, actual_list)
+ def test_write_cophenetic_and_inconsistency(self):
+ """Test to see if expected file is produced
+ """
+ actual_filename = "coph_incons.csv"
+ coph_out = linkagewriter.write_cophenetic_and_inconsistency(self.cophenetic_coefficient,
+ self.cophenetic_distance_matrix,
+ self.inconsistency_matrix,
+ actual_filename)
+ with open(self.expected_cop_filename, 'r') as exp_file:
+ exp_file_lines = exp_file.readlines()
+ with open(actual_filename, 'r') as act_file:
+ act_file_lines = act_file.readlines()
+ self.assertListEqual(act_file_lines, exp_file_lines)
+ def test_create_cophenetic_lines(self):
+ """Test to see if expected lines are produced.
+ """
+ expected_lines = [['Cophenetic coefficient', '0.7302032'],
+ ['Cophenetic Distance Matrix'],
+ ['0.0000000', '17.0000000', '33.0000000', '33.0000000', '22.0000000'],
+ ['17.0000000', '0.0000000', '33.0000000', '33.0000000', '22.0000000'],
+ ['33.0000000', '33.0000000', '0.0000000', '28.0000000', '33.0000000'],
+ ['33.0000000', '33.0000000', '28.0000000', '0.0000000', '33.0000000'],
+ ['22.0000000', '22.0000000', '33.0000000', '33.0000000', '0.0000000']]
+ actual_lines = linkagewriter.create_cophenetic_lines(self.cophenetic_coefficient,
+ self.cophenetic_distance_matrix)
+ self.assertListEqual(expected_lines, actual_lines)
+ def test_create_cophenetic_distance_line(self):
+ """Test to see if expected distance line is produced.
+ """
+ expected_line = ['0.0000000', '17.0000000', '33.0000000', '33.0000000', '22.0000000']
+ actual_line = linkagewriter.create_cophenetic_distance_line(np.array([0.0, 17., 33., 33., 22.]))
+ self.assertListEqual(expected_line, actual_line)
+ def test_create_inconsistency_lines(self):
+ """Test to see if expected list of lists is produced.
+ """
+ expected_lines = [['Mean Heights of links', 'SD for links',
+ 'Number of links', 'Inconsistency coefficient'],
+ ['17.0000000', '0.0000000', '1.0', '0.0000000'],
+ ['19.5000000', '3.5355340', '2.0', '0.7071070'],
+ ['28.0000000', '0.0000000', '1.0', '0.0000000'],
+ ['27.6666670', '5.5075710', '3.0', '0.9683640']]
+ actual_lines = linkagewriter.create_inconsistency_lines(self.inconsistency_matrix)
+ self.assertListEqual(expected_lines, actual_lines)
+ def test_create_inconsistency_line(self):
+ """Test to see if expected list is produced.
+ """
+ expected_line = ['17.0000000', '0.0000000', '1.0', '0.0000000']
+ actual_line = linkagewriter.create_inconsistency_line(self.inconsistency_matrix[0])
+ self.assertListEqual(expected_line, actual_line)
+
diff --git a/solventmapcreator/test/resources/expectedcopfile.csv b/solventmapcreator/test/resources/expectedcopfile.csv
new file mode 100644
index 0000000000000000000000000000000000000000..f4828b77694f90f0cb69fa7a341a8e5f96b4b6b5
--- /dev/null
+++ b/solventmapcreator/test/resources/expectedcopfile.csv
@@ -0,0 +1,12 @@
+Cophenetic coefficient 0.7302032
+Cophenetic Distance Matrix
+0.0000000 17.0000000 33.0000000 33.0000000 22.0000000
+17.0000000 0.0000000 33.0000000 33.0000000 22.0000000
+33.0000000 33.0000000 0.0000000 28.0000000 33.0000000
+33.0000000 33.0000000 28.0000000 0.0000000 33.0000000
+22.0000000 22.0000000 33.0000000 33.0000000 0.0000000
+Mean Heights of links SD for links Number of links Inconsistency coefficient
+17.0000000 0.0000000 1.0 0.0000000
+19.5000000 3.5355340 2.0 0.7071070
+28.0000000 0.0000000 1.0 0.0000000
+27.6666670 5.5075710 3.0 0.9683640