Add method to generate a formula whith combinations: negate explicitly other elements in the set

Makefile

@@ -32,7 +32,7 @@ t1:
 t2:
 	$(CMD_PYTHON) script_mac.py -vv debug compute_macs bio_models/pid_and_clock.bcx SRP9 --steps 7 --output p2
 t3:
-	$(CMD_PYTHON) script_mac.py -vv debug compute_macs bio_models/pid_or_clock.bcx SRP9 --steps 10 --output p3
+	$(CMD_PYTHON) script_mac.py -vv debug compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" SRP9 --all_macs --steps 10 --output p3
 t3bis:
 	$(CMD_PYTHON) script_mac.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" SRP9 --steps 10 --output p3bis
 t4:
@@ -44,7 +44,7 @@ t6:
 t7:
 	$(CMD_PYTHON) script_mac.py -vv debug compute_macs bio_models/pid_or_clock.bcx CCR5 --steps 7 --output p7
 real_study:
-	$(CMD_PYTHON) script_mac.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" --input_file --steps 7 --all_macs --input_file bio_models/input_places.txt --combinations
+	$(CMD_PYTHON) script_mac.py -vv info compute_macs "bio_models/Whole NCI-PID database translated into CADBIOM formalism(and).bcx" --steps 7 --all_macs --input_file bio_models/input_places.txt --combinations
 	
 	
 version:

script_cluster.sh

@@ -5,19 +5,14 @@
 #$ -cwd
 #$ -N cadbiom_analysis_dyliss
 #$ -j yes
-#$ -pe make 10
 
 # Demande de noeud sur le cluster
 #qrsh
 
 # Chargement de python 2
 .  /softs/local/env/envpython-2.7.sh
-.  /softs/local/env/envswig.sh
 .  /softs/local/env/envgcc-5.2.0.sh
-.  /softs/local/env/envcmake-3.4.3.sh
+#.  /softs/local/env/envswig.sh
+#.  /softs/local/env/envcmake-3.4.3.sh
 
 # Chargement de la tâche
-
-
-
-

script_mac.py

@@ -119,7 +119,7 @@ def main2(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_fil
     :param arg7: Formula: Property that the solver looks for.
     :param arg8: Formula: Original property (constraint) for the solver.
     :param arg9: Formula: ???
-    :param arg10: If set to True (not default), search allways macs with
+    :param arg10: If set to True (not default), search all macs with
         less or equal steps than previous, by limiting steps.
     :type arg1: <str>
     :type arg2: <str>
@@ -434,10 +434,26 @@ def compute_combinations(final_properties):
     :rtype: <list <str>>
     """
 
+    final_properties = set(final_properties)
+
+    def get_formula(data):
+        """Include all elements in the combinations and exclude explicitely,
+        all other elements.
+        """
+
+        negated_places = ' and not '.join(final_properties - data)
+        return "{}{}{}".format(
+                    ' and '.join(data),
+                    ' and not ' if negated_places != '' else '',
+                    negated_places
+                )
+
+
     all_combinations = list()
     for i in range(1, len(final_properties) + 1):
+
         all_combinations.append(
-            [' and '.join(comb) for comb in it.combinations(final_properties, i)]
+            {get_formula(set(comb)) for comb in it.combinations(final_properties, i)}
         )
 
     # Unpack combinations
@@ -449,6 +465,7 @@ def compute_combinations(final_properties):
     )
     LOGGER.info("Number of computed combinations: " + \
                 str(len(all_combinations)))
+
     return all_combinations