use pyasp-1.3.1

bioasp · Mar 6, 2014 · 59b3c56 · 59b3c56
1 parent 9243b49
commit 59b3c56
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Showing 3 changed files with 15 additions and 11 deletions.
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,7 +1,11 @@
-1.4
+v1.4.1
+----------------
+use pyasp-1.3.1
+
+v1.4
 ----------------
 use pyasp-1.3
 
-1.0 (unreleased)
+v1.0 (unreleased)
 ----------------
 Initial release
diff --git a/setup.py b/setup.py
@@ -33,7 +33,7 @@ def run(self):
 
 setup(cmdclass={'install': install},
       name='shogen',
-      version='1.4',
+      version='1.4.1',
       url='http://pypi.python.org/pypi/shogen/',
       license='GPLv3+',
       description='Finding shortest genome segments that regulate metabolic pathways',
@@ -45,6 +45,6 @@ def run(self):
       package_data = {'__shogen__' : ['encodings/*.lp']},
       scripts = ['shogen.py'],
       install_requires=[
-        "pyasp == 1.3"
+        "pyasp == 1.3.1"
       ]
 )
diff --git a/src/query.py b/src/query.py
@@ -63,7 +63,7 @@ def write(self,count, termset):
 def filter_couples(couple_facts, instance):
     prg = [filter_prg, instance, couple_facts.to_file()]
     solver = GringoClasp()
-    models = solver.run(prg,nmodels=0,collapseTerms=True, collapseAtoms=False)
+    models = solver.run(prg,collapseTerms=True, collapseAtoms=False)
     os.unlink(prg[2])
     return models[0]
 
@@ -76,7 +76,7 @@ def get_ksip_instance(instance, pmax):
     prg = [convert_prg , instance, inst ]
 
     solver = GringoClasp()
-    solution = solver.run(prg,1,collapseTerms=False, collapseAtoms=False)
+    solution = solver.run(prg,collapseTerms=False, collapseAtoms=False)
     os.unlink(inst)
     return solution[0] 
 
@@ -89,7 +89,7 @@ def get_sgs_instance(instance, pmax):
     prg = [convert_sds_prg , instance, inst ]
 
     solver = GringoClasp()
-    solution = solver.run(prg,1,collapseTerms=False, collapseAtoms=False)
+    solution = solver.run(prg,collapseTerms=False, collapseAtoms=False)
     os.unlink(inst)
     return solution[0] 
 
@@ -100,7 +100,7 @@ def preprocess(instance, start, goal, pmax):
     pmaxfact = String2TermSet('pmax('+str(pmax)+')')
     details = startfact.union(goalfact).union(pmaxfact)
     details_f = details.to_file() 
-    prg = [prepro_prg , instance, details_f ]
+    prg = [prepro_prg, instance, details_f ]
 
     solver = GringoClasp()
     solution = solver.run(prg,1)
@@ -126,12 +126,12 @@ def get_k_sgs(instance, start, end, pmax, k, dictg, revdictr):
     while count < k : 
       prg = [length_prg , instance, details_f ]
       goptions=' --const pmin='+str(min)
-      coptions='--opt-heu --opt-strategy=1 --heu=vsids'
+      coptions='--opt-heu --opt-strategy=1 --heu=vsids '
       #coptions='--opt-heu --heu=vsids'
       solver = GringoClasp(gringo_options=goptions,clasp_options=coptions)
       #solver = GringoUnClasp(gringo_options=goptions,clasp_options=coptions)
       #print "search1 ...",
-      optima = solver.run(prg,nmodels=0,collapseTerms=True,collapseAtoms=False)
+      optima = solver.run(prg,collapseTerms=True,collapseAtoms=False)
 
 
       if len(optima) :
@@ -144,7 +144,7 @@ def get_k_sgs(instance, start, end, pmax, k, dictg, revdictr):
 
 	prg = [length_prg , instance, details_f, exclude_sol([optima[0]]) ]
 	goptions='--const pmin='+str(min)
-	coptions='--opt-heu --opt-strategy=1 --opt-mode=optN'
+	coptions='--opt-heu --opt-strategy=1 --opt-mode=optN --opt-bound='+str(min)
 	solver = GringoClasp(gringo_options=goptions,clasp_options=coptions)
 	#print "search2 ...",
 	sols = solver.run(prg,collapseTerms=True,collapseAtoms=False)