permit alphanumerics, spaces, and underscores in flag strings

Author: jeff-k

pyvdrm/hcvr.py

@@ -328,7 +328,7 @@ def parser(self, rule):
                                           [(and_, 2, opAssoc.LEFT, AndExpr),
                                            (or_, 2, opAssoc.LEFT, OrExpr)]) | condition
 
-        score = Optional(Literal('-')) + integer | quote + Word(alphas) + quote
+        score = Optional(Literal('-')) + integer | quote + Regex(r'[a-zA-Z0-9 _]+') + quote
         scoreitem = booleancondition + mapper + score
         scoreitem.setParseAction(ScoreExpr)
         scorelist = max_ + l_par + delimitedList(scoreitem) + r_par |\

pyvdrm/tests/test_hcvr.py

@@ -108,11 +108,11 @@ def test_score_from_exactly(self):
         self.assertEqual(0, score)
 
     def test_score_comment(self):
-        rule = HCVR("SCORE FROM (100G => 10, 200T => 3, 100S => \"comment\")")
+        rule = HCVR("SCORE FROM (100G => 10, 200T => 3, 100S => \"flag1 with_space\")")
         self.assertEqual(rule(VariantCalls("100G")), 10)
         result = rule.dtree(VariantCalls("100S 200T"))
         self.assertEqual(result.score, 3)
-        self.assertTrue("comment" in result.flags)
+        self.assertTrue("flag1 with_space" in result.flags)
 
 class TestActualRules(unittest.TestCase):
     def test_hivdb_rules_parse(self):