reference files

tests/tests.py

@@ -31,7 +31,7 @@ def setUp(self):
         self.test_dir = tempfile.mkdtemp()
         os.chdir(self.test_dir)
         self.c = YGtPM()
-        self.store_ref = False
+        # self.store_ref = False
         # at various places out put is compared to stored reference files. put this to true
         # to regenerate all reference files
 
@@ -44,39 +44,26 @@ def test_class_creation(self):
         testing the creation of YGtPM
         """
         self.assertIsInstance(self.c, YGtPM)
+        self.c.pTMdata()
+        self.assertTrue(os.path.isfile('uniprot_mod_raw.txt'))
 
     def test_data(self):
         """
         testing the steps in data()
         """
-        self.assertIsInstance(self.c, YGtPM)
-        try:  # the actual download can only be performed a limit number of times per hour
-            raise RuntimeError  # this is to prevent connecting the database during development comment for real tesing
-            self.c.pTMdata()
-            if self.store_ref:
-                shutil.copy('uniprot_mod_raw.txt', ref_dir)  # saving the reference data
-        except:
-            shutil.copy(os.path.join(ref_dir, 'uniprot_mod_raw.txt'), '.')
-        self.assertTrue(os.path.isfile('uniprot_mod_raw.txt'))
-        self.c.clean('uniprot_mod_raw.txt')  # produces PTMs.txt
+        shutil.copy(os.path.join(ref_dir, 'uniprot_mod_raw.txt'), '.')  # saving the reference data
 
+        self.c.clean('uniprot_mod_raw.txt')  # produces PTMs.txt
         self.assertTrue(os.path.isfile('PTMs.txt'))
-        if self.store_ref:
-            shutil.copy('PTMs.txt', ref_dir)  # saving the reference data
         self.assertTrue(filecmp.cmp('PTMs.txt', os.path.join(ref_dir, 'PTMs.txt')))
 
         self.c.iD()
         self.assertTrue(os.path.isfile('yeastID.txt'))
-        if self.store_ref:
-            shutil.copy('yeastID.txt', ref_dir)  # saving the reference data
         self.assertTrue(filecmp.cmp('yeastID.txt', os.path.join(ref_dir, 'yeastID.txt')))
 
         self.c.pmap('yeastID.txt', 'PTMs.txt')
         self.assertTrue(os.path.isfile('PTM_id_file.txt'))
-        if self.store_ref:
-            shutil.copy('PTM_id_file.txt', ref_dir)  # saving the reference data
         self.assertTrue(filecmp.cmp('PTM_id_file.txt', os.path.join(ref_dir, 'PTM_id_file.txt')))
-        self.assertTrue(False)
 
     def test_ymap_proteins(self):
         self.assertTrue(True)

ymap/ymap.py

@@ -31,14 +31,14 @@
 from __future__ import absolute_import
 from __future__ import division
 from __future__ import unicode_literals
-#try:
-#    from builtins import next
-#    from builtins import str
-#    from builtins import range
-#    from builtins import object
-#    from builtins import bytes
-#except ImportError:
-#    pass
+try:
+    from builtins import next
+    from builtins import str
+    from builtins import range
+    from builtins import object
+    from builtins import bytes
+except ImportError:
+    pass
 import os
 import sys
 import math
@@ -1050,27 +1050,27 @@ def data():
     except IOError:
         pass
     try:
-        m = c.pmap('yeastID.txt', 'PTMs.txt')
+        c.pmap('yeastID.txt', 'PTMs.txt')
     except IOError:
         pass
     try:
-        d = c.dclean('uniprot_mod_raw.txt')
+        c.dclean('uniprot_mod_raw.txt')
     except IOError:
         pass
     try:
-        dm = c.d_map('yeastID.txt', 'domains.txt')
+        c.d_map('yeastID.txt', 'domains.txt')
     except IOError:
         pass
     try:
-        ab = c.ab('uniprot_mod_raw.txt')
+        c.ab('uniprot_mod_raw.txt')
     except IOError:
             pass
     try:
-        ii = c.id('bact.txt', 'yeast_id.txt')
+        c.id('bact.txt', 'yeast_id.txt')
     except IOError:
             pass
     try:
-        bio=c.bioGrid()
+        c.bioGrid()
     except IOError:
             pass
     try:
@@ -1696,4 +1696,3 @@ def path():
             pass
     else:
         print ("to run a function seek help")
-