Add ability to view gene rule using name

This is the new gene_name_reaction_rule attribute.

Fixes #174

cobra/core/Gene.py

@@ -27,18 +27,31 @@
 
 
 # functions for gene reaction rules
-def ast2str(expr, level=0):
-    """convert compiled ast to gene_reaction_rule str"""
+def ast2str(expr, level=0, names=None):
+    """convert compiled ast to gene_reaction_rule str
+
+    expr: str of a gene reaction rule
+
+    level: internal use only
+
+    names: optional dict of {Gene.id: Gene.name}
+        Use this to get a rule str which uses names instead. This
+        should be done for display purposes only. All gene_reaction_rule
+        strings which are computed with should use the id.
+    """
     if isinstance(expr, Expression):
-        return ast2str(expr.body, 0) if hasattr(expr, "body") else ""
+        return ast2str(expr.body, 0, names) \
+            if hasattr(expr, "body") else ""
     elif isinstance(expr, Name):
-        return expr.id
+        return names.get(expr.id, expr.id) if names else expr.id
     elif isinstance(expr, BoolOp):
         op = expr.op
         if isinstance(op, Or):
-            str_exp = " or ".join(ast2str(i, level + 1) for i in expr.values)
+            str_exp = " or ".join(ast2str(i, level + 1, names)
+                                  for i in expr.values)
         elif isinstance(op, And):
-            str_exp = " and ".join(ast2str(i, level + 1) for i in expr.values)
+            str_exp = " and ".join(ast2str(i, level + 1, names)
+                                   for i in expr.values)
         else:
             raise TypeError("unsupported operation " + op.__class__.__name)
         return "(" + str_exp + ")" if level else str_exp

cobra/core/Reaction.py

@@ -8,7 +8,7 @@
 from six import string_types, iteritems
 
 from .Object import Object
-from .Gene import Gene, parse_gpr
+from .Gene import Gene, parse_gpr, ast2str
 from .Metabolite import Metabolite
 
 
@@ -125,6 +125,19 @@ def gene_reaction_rule(self, new_rule):
                     warn("could not remove old gene %s from reaction %s" %
                          (g.id, self.id))
 
+    @property
+    def gene_name_reaction_rule(self):
+        """Display gene_reaction_rule with names intead.
+
+        Do NOT use this string for computation. It is intended to give a
+        representation of the rule using more familiar gene names instead of
+        the often cryptic ids.
+
+        """
+        names = {i.id: i.name for i in self._genes}
+        ast = parse_gpr(self._gene_reaction_rule)[0]
+        return ast2str(ast, names=names)
+
     @property
     def x(self):
         """The flux through the reaction in the most recent solution

cobra/test/unit_tests.py

@@ -253,6 +253,8 @@ def testGPR_modification(self):
         fake_gene = model.genes.get_by_id("fake_gene")
         self.assertIn(fake_gene, reaction.genes)
         self.assertIn(reaction, fake_gene.reactions)
+        fake_gene.name = "foo_gene"
+        self.assertEqual(reaction.gene_name_reaction_rule, fake_gene.name)
 
     def test_add_metabolite(self):
         """adding a metabolite to a reaction in a model"""
@@ -291,6 +293,7 @@ def test_build_from_string(self):
         self.assertEqual(pgi.lower_bound, 0)
         pgi.reaction = "g6p_c <== f6p_c"
         self.assertEqual(pgi.upper_bound, 0)
+        self.assertEqual(pgi.reaction.strip(), "g6p_c <-- f6p_c")
         pgi.reaction = "g6p_c --> f6p_c + h2o_c"
         self.assertIn(model.metabolites.h2o_c, pgi._metabolites)
         pgi.build_reaction_from_string("g6p_c --> f6p_c + foo", verbose=False)