Changeset 107 for biocomp.pscoils/trunk/tests/tests_coils.py

Timestamp:

10/18/09 19:27:54 (3 years ago)

Author:

mauro

Message:

pre tag 1.0.0

Location:

biocomp.pscoils/trunk

Files:

• . (modified) (1 prop)
• tests/tests_coils.py (modified) (3 diffs)

biocomp.pscoils/trunk/tests/tests_coils.py

@@ -3 +3 @@
 from unittest import TestCase
 import StringIO
-import biocomp.pscoils
+from biocomp.pscoils import pred_coil
+from biocomp.pscoils.utils import readFasta, printCoil
+from biocomp.pscoils.Params import Params
+from Bio.SeqRecord import SeqRecord
 
 class test_suite(TestCase):
@@ -12 +15 @@
         win=21
         modeprofile=False
-        seqs=biocomp.pscoils.readFasta("tests/ferritin.fasta")
+        seqs=readFasta("tests/ferritin.fasta")
         modefasta=True
         labels='F'
-        params=biocomp.pscoils.Params.Params(weight,win)
+        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)
+            seqr = SeqRecord(seqs[name], id=name)
+            seqr = pred_coil(seqr, params)
+            printCoil(seqr,labels,io=output)
         bench_output = open("tests/ferritin.Coils").read()
         self.assertEqual(output.getvalue(),bench_output)        
@@ -29 +33 @@
         win=21
         modeprofile=False
-        seqs=biocomp.pscoils.readFasta("tests/ceba_bovin.fasta")
+        seqs=readFasta("tests/ceba_bovin.fasta")
         modefasta=True
         labels='F'
-        params=biocomp.pscoils.Params.Params(weight,win)
+        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)
+            seqr = SeqRecord(seqs[name], id=name)
+            seqr = pred_coil(seqr, params)
+            printCoil(seqr,labels,io=output)
         bench_output = open("tests/ceba_bovin.Coils").read()
         self.assertEqual(output.getvalue(),bench_output)