fixed duplicate functions

ClassDefinitions.py

@@ -209,6 +209,8 @@ def addReaction(self, reactionName, reactionPairs, reversible = False, descripti
         self.createMatrices()
         self.updateReduction()
     def deleteMetabolites(self, metaboliteIndices):
+        assert min(metaboliteIndices) >= 0
+        assert max(metaboliteIndices) < len(self.metabolites)
         self.metabolites = [m for i, m in enumerate(self.metabolites) if i not in metaboliteIndices]
         self.createMatrices()
         self.updateReduction()
@@ -264,6 +266,8 @@ def findMinimalMedia(self):
         Exch = sum([Exch[x] for x in range(6) if x != 2], []) # omit irreversible export reactions
         return findMinimalMedia(N, biomassIndex, Exch, rec = False, I = Irr)
     def printReactionFormula(self, reactionNumber):
+        assert reactionNumber > 0
+        assert reactionNumber < len(self.reactions)
         curReact = self.reactions[reactionNumber]
         curPairs = curReact.pairs
         curMetabs = self.metabolites

LegacyCode.py

@@ -200,4 +200,38 @@ def rankList(values, reverse = False):
     # Ties are broken in a stable way; if reverse is True, ranks are reversed.
     myList = [(values[x],x) for x in range(len(values))]
     myList = sorted(myList, reverse = reverse)
-    return [x[1] for x in myList]
+    return [x[1] for x in myList]
+
+def classifyExchange(FullNetwork, externalMetabs, Irrev):
+    # This function finds all the exchange reactions in a given full network
+    # (with the external metabolites included) and classifies them into 3 types:
+    # input only, output only, and mixed, and additionally by irreversibility.
+    m = len(FullNetwork)
+    n = len(FullNetwork[0])
+    Exchange = [y for y in range(n) if [_f for _f in [FullNetwork[x][y] for x in externalMetabs] if _f]]
+    InputIrr, InputRev, OutputIrr, OutputRev, MixedIrr, MixedRev = [], [], [], [], [], []
+    for react in Exchange:
+        In, Out = False, False
+        for x in externalMetabs:
+            if FullNetwork[x][react] < 0:
+                In = True
+            elif FullNetwork[x][react] > 0:
+                Out = True
+        if In and Out:
+            if react in Irrev:
+                MixedIrr.append(react)
+            else:
+                MixedRev.append(react)
+        elif In and (not Out):
+            if react in Irrev:
+                InputIrr.append(react)
+            else:
+                InputRev.append(react)
+        elif (not In) and Out:
+            if react in Irrev:
+                OutputIrr.append(react)
+            else:
+                OutputRev.append(react)
+        else:
+            print('This should never happen!')
+    return (InputIrr, InputRev, OutputIrr, OutputRev, MixedIrr, MixedRev)

ModelProcessing.py

@@ -1378,7 +1378,7 @@ def findEssentialLethal(Network, Target, Filename = 'lethal.lp', rec = True, I =
     if verbose:
         print(('There are ' + str(len(CandidatePairs)) + ' pairs to be processed'))
     for ind, pair in enumerate(CandidatePairs):
-        if verbose and (ind + 1) % 100 == 0:
+        if verbose and (ind + 1) % 1000 == 0:
             print(('Processed ' + str(ind + 1) + ' pairs so far'))
         if all([(pair[0] in z or pair[1] in z) for z in Collection]):
             if testCutSet(pair, Network, Target, Filename[:-3] + str(Iter) + Filename[-3:], rec, I):

Unrelated.py

@@ -5,40 +5,6 @@
 from GeneProcessing import *
 from functools import reduce
 
-def classifyExchange(FullNetwork, externalMetabs, Irrev):
-    # This function finds all the exchange reactions in a given full network
-    # (with the external metabolites included) and classifies them into 3 types:
-    # input only, output only, and mixed, and additionally by irreversibility.
-    m = len(FullNetwork)
-    n = len(FullNetwork[0])
-    Exchange = [y for y in range(n) if [_f for _f in [FullNetwork[x][y] for x in externalMetabs] if _f]]
-    InputIrr, InputRev, OutputIrr, OutputRev, MixedIrr, MixedRev = [], [], [], [], [], []
-    for react in Exchange:
-        In, Out = False, False
-        for x in externalMetabs:
-            if FullNetwork[x][react] < 0:
-                In = True
-            elif FullNetwork[x][react] > 0:
-                Out = True
-        if In and Out:
-            if react in Irrev:
-                MixedIrr.append(react)
-            else:
-                MixedRev.append(react)
-        elif In and (not Out):
-            if react in Irrev:
-                InputIrr.append(react)
-            else:
-                InputRev.append(react)
-        elif (not In) and Out:
-            if react in Irrev:
-                OutputIrr.append(react)
-            else:
-                OutputRev.append(react)
-        else:
-            print('This should never happen!')
-    return (InputIrr, InputRev, OutputIrr, OutputRev, MixedIrr, MixedRev)
-
 def findReachable(Network, Inputs, Allowed):
     # This function finds the reachable reactions and metabolites in a metabolic network
     # given a set of input reactions and a subset of allowed input reactions (all other