L statistic window

Author: PeterDulworth

CommandLineFiles/CalculateGeneralizedDStatistic.py

@@ -1272,3 +1272,31 @@ def calculate_generalized(alignment, species_tree, reticulations, verbose=False)
 print trees_of_interest
 increase, decrease = determine_patterns(trees_of_interest, trees_to_equality, patterns_pgN)
 print generate_statistic_string((increase, decrease))
+
+
+## Changing Network to Species Tree
+def network_to_species_tree(network):
+    """
+
+    :param network:
+    :return:
+    """
+    # remove H1...
+    spec1 = re.sub('(#H\d\W\d\W+\d.\d+\W+)', '', network)
+    print spec1
+    # remove extra parentheses - this is v good
+    spec2 = re.sub('\((P\d+)\)', r'\1 ', spec1)
+    print spec2
+    # adds colon back in?? bad probably
+    spec3 = re.sub(' ', ':', spec2)
+    print spec3
+    # removes extras again?? this is bad
+    spec4 = re.sub('(,\()', ',', spec3)
+    print spec4
+    # removes extra colons
+    spectree = re.sub('(::)', ':', spec4)
+
+    return spectree
+
+print 'output', network_to_species_tree(network)
+print "should be", species_tree

main.py

@@ -247,6 +247,17 @@ def displayDStatistic(self, dVal, dWindows):
         self.dStatisticLabel.setEnabled(True)
         self.dStatisticValueLabel.setEnabled(True)
 
+    # **************************** L STATISTIC PAGE ****************************#
+
+    def displayLStatistic(self, lVal, lWindows):
+        self.lVal = lVal
+        self.lWindows = lWindows
+        self.lStatisticWindow = dStatisticWindow.DStatisticWindow(self.lWindows)
+
+        self.lStatisticValueLabel.setText(str(self.lVal))
+        self.lStatisticLabel.setEnabled(True)
+        self.lStatisticValueLabel.setEnabled(True)
+
     # **************************** MS PAGE ****************************#
 
     additionalFileCounter = 0

raxmlOutputWindows/lStatisticWindow.py

@@ -0,0 +1,32 @@
+from standardWindow import Window
+from PyQt4 import QtGui
+import sys
+
+"""
+D-Statistic Window
+~
+Chabrielle Allen
+Travis Benedict
+Peter Dulworth
+"""
+
+class LStatisticWindow(Window):
+    def __init__(self, lWindows, title='Windows to L Statistic', xLabel='Window Indices', yLabel='L Statistic values'):
+        Window.__init__(self, windowTitle='L Statistic Window')
+
+        self.plotter.stat_scatter(lWindows, title, xLabel=xLabel, yLabel=yLabel)
+        self.show()
+
+
+if __name__ == '__main__': # only runs if not imported
+
+    # create a new instance of QApplication
+    app = QtGui.QApplication(sys.argv)
+
+    a = {0:0, 2:2, 4:3}
+
+    # create window and plot
+    form = LStatisticWindow(a)
+
+    # execute the app
+    sys.exit(app.exec_())

test_module/test_RAxMLOperations.py

@@ -8,7 +8,8 @@ def test_taxon_names_getter(self):
         self.assertEqual(["Seq0", "Seq1", "Seq2", "Seq3"], raxOps.taxon_names_getter("../exampleFiles/2basePhylip.txt"))
 
     def test_raxml_species_tree(self):
-        self.fail()
+        raxOps = RAxMLOperations.RAxMLOperations()
+        print raxOps.raxml_species_tree("../exampleFiles/2basePhylip.txt")
 
     def test_rooter(self):
         self.fail()