Final version with multi processing implemented

WGS-TB · Mar 16, 2017 · af1e9a5 · af1e9a5
1 parent f5234a4
commit af1e9a5
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Showing 3 changed files with 27 additions and 22 deletions.
diff --git a/ClassDefinitions.py b/ClassDefinitions.py
@@ -241,13 +241,13 @@ def findEssentialReactions(self):
                 print(('There are ' + str(numBasicEssential - 1) + ' essential reactions in a subset with the growth reaction.'))
                 print('Returning the remaining essential reactions')
                 return sorted(EssentialFull)
-    def findSyntheticLethalPairs(self):
+    def findSyntheticLethalPairs(self,parallel=0):
         if self.checkReduced():
             Network = self.reducedMatrix
             Target = self.findBiomassReactionReduced()
             if Target is not None:
                 Irr = [i for i, subset in enumerate(self.reactionSubsets) if not subset.reversible]
-                Essential, Lethal = findEssentialLethal(Network, Target, rec = False, I = Irr, verbose = True)
+                Essential, Lethal = findEssentialLethal(Network, Target, rec = False, I = Irr, verbose = True,parallel=parallel)
                 allPairs = []
                 for item in Lethal:
                     first, second = item[0], item[1]

diff --git a/MONGOOSEgui.py b/MONGOOSEgui.py
@@ -109,7 +109,7 @@ def run(self):
             print(getattr(self.model_name, self.function_name)())
             print(time.time() - start_time)
         elif(self.index_name == self.findSyntheticLethalPairs):
-            print(getattr(self.model_name, self.function_name)())
+            print(getattr(self.model_name, self.function_name)(0))
             print(time.time() - start_time)
         else:
             print("Thread could not find work")
@@ -261,6 +261,7 @@ def setupUi(self, MainWindow):
         self.chooseParallel.setObjectName(_fromUtf8("chooseIndex"))
         self.chooseParallel.setPlaceholderText('threads')
         self.chooseParallel.setVisible(False)
+        self.chooseParallel.setToolTip(_translate("MainWindow", "<html><head/><body><p>Choose the number of threads</p></body></html>", None))
 
         # intializes third dropdown menu, chooses a function
         self.chooseFunction3 = QtGui.QComboBox(self.centralwidget)
@@ -537,7 +538,7 @@ def hide1(self):
             if(index == PRINT_RXN_FORMULA or index==DELETE_RXN or index==DELETE_METAB):
                 self.chooseIndex.setVisible(True)
                 self.chooseParallel.setVisible(False)
-            elif(index == REDUCE_NETWORK or index == FIND_SYNTH_LETH_PAIRS):
+            elif(index == FIND_SYNTH_LETH_PAIRS):
                 self.chooseIndex.setVisible(False)
                 self.chooseParallel.setVisible(True)
             elif(index == ADD_RXN or index == ADD_METAB):
@@ -733,18 +734,28 @@ def chooseFunction(self):
                     print(">>> model.%s()" % (function1))
                     if(index1 == REDUCE_NETWORK):
                         print("Reducing network")
-                        #self.myThread = WorkerThread(model,function1, REDUCE_NETWORK)
+                        self.myThread = WorkerThread(model,function1, REDUCE_NETWORK)
                         start_time = time.time()
-                        #self.myThread.start()
-                        print(getattr(model, function1)())
-                        print(time.time() - start_time)
+                        self.myThread.start()
+                        #print(getattr(model, function1)())
+                        #print(time.time() - start_time)
                     elif(index1 == FIND_SYNTH_LETH_PAIRS):
-                        print("Finding synthetic lethal pairs")
-                        #self.myThread = WorkerThread(model,function1, FIND_SYNTH_LETH_PAIRS)
-                        start_time = time.time()
-                        print(getattr(model, function1)())
-                        #self.myThread.start()
-                        print(time.time() - start_time)
+                        numProc = self.chooseParallel.text()
+                        if numProc:
+                            print("Finding synthetic lethal pairs")
+                            numProc = int( numProc )
+                            start_time = time.time()
+                            print(getattr(model, function1)(numProc))
+                            print(time.time() - start_time)
+                        elif(numProc == 0):
+                            print("Finding synthetic lethal pairs")
+                            self.myThread = WorkerThread(model,function1, FIND_SYNTH_LETH_PAIRS)
+                            self.myThread.start()
+                        else:
+                            numProc = 0
+                            print("Finding synthetic lethal pairs")
+                            self.myThread = WorkerThread(model,function1, FIND_SYNTH_LETH_PAIRS)
+                            self.myThread.start()
                     else:
                         print(getattr(model, function1)())
 

diff --git a/ModelProcessing.py b/ModelProcessing.py
@@ -9,11 +9,7 @@
 from math import gcd
 from fractions import Fraction
 from Utilities import *
-#from multiprocessing import Process, Queue
 import multiprocessing
-#import queue
-#from multiprocessing import Pool # threading
-#from multiprocessing.dummy import Pool as ThreadPool # threading
 
 zero, one = Fraction(0), Fraction(1)
 
@@ -713,7 +709,6 @@ def findDistance(N, special, Irrev, norm = 'inf'):
 
 ####parallelization
 def parallelizedNegFindFeasible(N, Irrev, pos  ,index, option,subList,out_q_neg):
-    #subOnlyNeg = []
     count = len(subList) * index
     outdict = {}
     for ind, react in enumerate(subList): # changed from subOnlyNeg to subList!
@@ -723,7 +718,6 @@ def parallelizedNegFindFeasible(N, Irrev, pos  ,index, option,subList,out_q_neg)
     out_q_neg.put(outdict) #places dictionary into queue asynchronously
 
 def parallelizedPosFindFeasible(N, Irrev, pos  ,index, option,subList,out_q_pos):
-    #subOnlyPos = []
     outdict = {}
     count = len(subList) * index
     for ind, react in enumerate(subList):# changed from subOnlyPos to subList!
@@ -748,7 +742,7 @@ def findUnidirectional(N, Irrev, option = 'null', verbose = False, parallel = 0)
     canBeNegative = findTBlocked(N, allRev, basename = 'canBeNegative.lp', restricted = False, option = option, rev = True, negated = True)
     onlyPosCandidates = [i for i in allRev if i not in canBeNegative]
     onlyNegCandidates = [i for i in allRev if i not in canBePositive]
-    parallel = 6 #testing
+    parallel = 0 #testing
 
     if len(onlyNegCandidates) <= 1:
         onlyNeg = onlyNegCandidates
@@ -1544,7 +1538,7 @@ def findEssentialLethal(Network, Target, Filename = 'lethal.lp', rec = True, I =
     CandidatePairs = [[x,y] for x in allCandidates for y in allCandidates if x < y]
     if verbose:
         print(('There are ' + str(len(CandidatePairs)) + ' pairs to be processed'))
-    parallel = 6 # testing
+    #parallel = 6 # testing
     if parallel > 0:
         CandidatePairs = [pair for pair in CandidatePairs if all([(pair[0] in z or pair[1] in z) for z in Collection])]
         splitPairs = [CandidatePairs[i::parallel] for i in range(parallel)]