ex-236 (cgates): adjust glossary to work in py3

umich-brcf-bioinf · May 5, 2015 · 580ae50 · 580ae50
1 parent 2157808
commit 580ae50
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/jacquard/expand.py b/jacquard/expand.py
@@ -165,7 +165,7 @@ def validate_args(args):
 def _get_actual_columns(vcf_reader, col_spec):
     columns  = _create_potential_column_list(vcf_reader)
     glossary_fields = []
-    for glossary_field in sorted(columns.values()):
+    for glossary_field in sorted([x for x in columns.values() if x]):
         if glossary_field and glossary_field not in glossary_fields:
             glossary_fields.append(glossary_field)
 

diff --git a/test/expand_test.py b/test/expand_test.py
@@ -185,7 +185,7 @@ def test_create_potential_column_list_preservesSampleOrdering(self):
                                         sample_names=sample_names)
 
         actual_cols = expand._create_potential_column_list(mock_vcf_reader)
-        actual_format_sample_names = actual_cols.keys()[8:]
+        actual_format_sample_names = list(actual_cols.keys())[8:]
 
         expected_format_sample_names = ["A|sample1", "A|sample2", "A|sample10",
                                         "B|sample1", "B|sample2", "B|sample10"]