Merge branch 'master' of https://github.com/bartongroup/ProteoFAV

bartongroup · Feb 21, 2018 · a4d4e0a · a4d4e0a
2 parents dad1338 + ba7768a
commit a4d4e0a
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/proteofav/structures.py b/proteofav/structures.py
@@ -326,6 +326,7 @@ def _add_mmcif_res_full(table):
     :return: returns a modified pandas DataFrame
     """
 
+    table.is_copy = False
     # adds both 'label' and 'auth' entries
     if 'label_seq_id' in table:
         table['label_seq_id_full'] = (table['label_seq_id'] +
@@ -410,7 +411,7 @@ def _remove_multiple_altlocs(table):
         altloc = table.loc[ix, 'label_alt_id']
         if altloc != '.':
             # table.loc[ix, 'label_alt_id'] = '.'
-            table.set_value(ix, 'label_alt_id', '.')
+            table.at[ix, 'label_alt_id'] = '.'
             atomid = table.loc[ix, 'label_atom_id']
             try:
                 for nx in range(1, 100, 1):

diff --git a/proteofav/variants.py b/proteofav/variants.py
@@ -911,7 +911,7 @@ def _fetch_icgc_variants(identifier):
                     ' Duplicated index for {}.'.format(identifier))
     else:
         data = data.join(consequence.apply(pd.Series), rsuffix='_protein')
-        transition = data.aaMutation.str.extract(transition_regex)
+        transition = data.aaMutation.str.extract(transition_regex, expand=False)
         data = data.join(transition)
 
     return data
diff --git a/tests/test_variants.py b/tests/test_variants.py
@@ -485,7 +485,8 @@ def test_fetch_ensembl_uniprot_mapping(self):
         r = self.fetch_ensembl_uniprot_mapping(self.ensembl_id2)
         self.assertTrue(r.ok)
         uniprots = self.get_uniprot_id_from_mapping(r.json())
-        self.assertEqual(uniprots, ['A0A024RBG4', self.uniprot_id2])
+        self.assertIn('A0A024RBG4', uniprots)
+        self.assertIn(self.uniprot_id2, uniprots)
 
     def test_to_table_uniprot_ensembl_mapping_full(self):
         """
@@ -534,7 +535,8 @@ def test_get_uniprot_id_from_mapping(self):
 
         r = self.get_uniprot_id_from_mapping(data.json(), full_entry=False,
                                              uniprot_id=None)
-        self.assertEqual(r, ['A0A024RBG4', self.uniprot_id2])
+        self.assertIn('A0A024RBG4', r)
+        self.assertIn(self.uniprot_id2, r)
 
         r = self.get_uniprot_id_from_mapping(data.json(), full_entry=True,
                                              uniprot_id=None)