Use - and + instead of * and !

sanger-pathogens · Jul 28, 2016 · fe6fce5 · fe6fce5
1 parent 6995ab6
commit fe6fce5
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Showing 3 changed files with 10 additions and 9 deletions.
diff --git a/ariba/ref_preparer.py b/ariba/ref_preparer.py
@@ -72,16 +72,16 @@ def _rename_clusters(clusters_in):
             elif len(names_before_dots) == 1:
                 new_key = list(names_before_dots.keys())[0]
                 if sum(list(names_before_dots.values())) < len(name_set):
-                    new_key += '!'
+                    new_key += '+'
             else:
                 common_prefix = os.path.commonprefix(list(names_before_dots.keys()))
                 if common_prefix == '' or len(common_prefix) < min_prefix_length:
                     max_value = max(list(names_before_dots.values()))
                     possible_keys = [x for x in names_before_dots if names_before_dots[x] == max_value]
                     possible_keys.sort()
-                    new_key = possible_keys[0] + '!'
+                    new_key = possible_keys[0] + '+'
                 else:
-                    new_key = common_prefix + '*'
+                    new_key = common_prefix + '-'
 
             if new_key in key_count:
                 if new_key in new_clusters:

diff --git a/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv b/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv
@@ -1,5 +1,5 @@
 cluster_1	gene1	gene2
 cluster_2	gene3
 gene4	gene4.var_only
-noncoding*	noncoding1	noncoding2.var_only	noncoding3.var_only
+noncoding-	noncoding1	noncoding2.var_only	noncoding3.var_only
 noncoding4	noncoding4.var_only
diff --git a/ariba/tests/ref_preparer_test.py b/ariba/tests/ref_preparer_test.py
@@ -29,14 +29,15 @@ def test_rename_clusters(self):
             'cluster_2': {'another_no_dot_in_name'},
             'foo_1': {'foo.blah_blah_blah', 'foo.xyz'},
             'foo_2': {'foo.abc', 'foo.def'},
-            'pre*_1': {'pre1.abc', 'pre2.abc'},
-            'pre*_2': {'pre1.def', 'pre2.pqr', 'pre2.zxy'},
-            'prefix1!_1': {'prefix1.abc', 'prefix1.def', 'something_else.abc'},
-            'prefix1!_2': {'prefix1.fgh', 'prefix1.ijk', 'something_else_again.abc'},
-            'xyz!': {'xyz.1', 'xyz.2', 'abcdefgh'},
+            'pre-_1': {'pre1.abc', 'pre2.abc'},
+            'pre-_2': {'pre1.def', 'pre2.pqr', 'pre2.zxy'},
+            'prefix1+_1': {'prefix1.abc', 'prefix1.def', 'something_else.abc'},
+            'prefix1+_2': {'prefix1.fgh', 'prefix1.ijk', 'something_else_again.abc'},
+            'xyz+': {'xyz.1', 'xyz.2', 'abcdefgh'},
             'cluster_3': {'a.foo', 'a.bar'},
         }
 
+        self.maxDiff = None
         got = ref_preparer.RefPreparer._rename_clusters(clusters_in)
         self.assertEqual(expected, got)