Merge pull request #240 from jonls/fastgapfill-epsilon

fastgapfill: Fix bug where epsilon was not used
zhanglab · May 19, 2017 · 6a6232e · 6a6232e
2 parents edace45 + 862623d
commit 6a6232e
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/psamm/fastgapfill.py b/psamm/fastgapfill.py
@@ -51,7 +51,7 @@ def fastgapfill(model_extended, core, solver, weights={}, epsilon=1e-5):
     # Run Fastcore and print the induced reaction set
     logger.info('Calculating Fastcore induced set on model')
     induced = fastcore(
-        model_extended, core, epsilon=1e-5, weights=weights, solver=solver)
+        model_extended, core, epsilon=epsilon, weights=weights, solver=solver)
     logger.debug('Result: |A| = {}, A = {}'.format(len(induced), induced))
     added_reactions = induced - core
     logger.debug('Extended: |E| = {}, E = {}'.format(