Merge pull request #18 from cdanielmachado/development

merge development branch

carveme/reconstruction/carving.py

@@ -242,7 +242,7 @@ def carve_model(model, reaction_scores, outputfile=None, flavor=None, inplace=Tr
         r_id = row['reaction']
         if r_id in model.reactions:
             try:
-                gpr = parse_gpr_rule(row['GPR'])
+                gpr = parse_gpr_rule(row['GPR'], prefix='G_')
                 model.set_gpr_association(r_id, gpr, add_genes=True)
             except:
                 print 'Failed to parse:', row['GPR']

carveme/reconstruction/scoring.py

@@ -11,7 +11,9 @@ def merge_subunits(genes):
         str: boolean rule
 
     """
-    if any(genes.isnull()):
+    genes = genes.dropna()
+
+    if len(genes) == 0:
         return None
     else:
         protein = ' and '.join(sorted(genes))
@@ -23,8 +25,7 @@ def merge_subunits(genes):
 
 def merge_subunit_scores(scores):
     """ Merge scores of all genes in a protein complex.
-    Calculates the minimum score among all subunits.
-    If any subunit is missing (NaN) the result is NaN.
+    Calculates the mean score among all subunits.
 
     Args:
         scores: individual gene scores
@@ -33,7 +34,8 @@ def merge_subunit_scores(scores):
         float: merged score
 
     """
-    return scores.min(skipna=False)
+
+    return scores.fillna(0).mean()
 
 
 def merge_proteins(proteins):

scripts/carve

@@ -191,6 +191,8 @@ def main(inputfile, input_type='protein', outputfile=None, diamond_args=None, un
                                 init_env=init_env,
                                 debug_output=debug_output)
     else:
+        if verbose:
+            print 'Building an ensemble of', ensemble_size, 'models'
         build_ensemble(universe_model, scores, ensemble_size, outputfile, flavor, init_env=init_env)
 
     if gapfill and model is not None: