Changeset 10 for biocomp.pscoils

Timestamp:

02/16/08 10:00:35 (4 years ago)

Author:

mauro

Message:

 

Location:

biocomp.pscoils/trunk

Files:

• src (modified) (1 prop)
• tests/ceba_bovin.Coils (added)
• tests/ceba_bovin.fasta (added)
• tests/tests_coils.py (moved) (moved from biocomp.pscoils/trunk/tests/test_ferritin.py) (2 diffs)

biocomp.pscoils/trunk/tests/tests_coils.py

@@ -6 +6 @@
 
 class test_suite(TestCase):
-    def test_coils(self):
+    def test_ferritin(self):
         # ../psCoils.py -f ./ferritin.fasta -l F > ./ferritin.Coils
         weight='un'
@@ -22 +22 @@
         bench_output = open("tests/ferritin.Coils").read()
         self.assertEqual(output.getvalue(),bench_output)        
+        
+    def test_ceba_bovin(self):
+        # ../psCoils.py -f ./ferritin.fasta -l F > ./ferritin.Coils
+        weight='un'
+        wlambda=0.5
+        win=21
+        modeprofile=False
+        seqs=biocomp.pscoils.readFasta("tests/ceba_bovin.fasta")
+        modefasta=True
+        labels='F'
+        params=biocomp.pscoils.Params.Params(weight,win)
+        output = StringIO.StringIO()
+        for name in seqs.keys():
+            gg,gcc,prob,hept_seq,score=biocomp.pscoils.pred_coil(seqs[name],len(seqs[name]),params,biocomp.pscoils.seqScore)
+            biocomp.pscoils.printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels,io=output)
+        bench_output = open("tests/ceba_bovin.Coils").read()
+        self.assertEqual(output.getvalue(),bench_output)        
 
 if __name__ == "__main__":