Updated memory handling

KarchinLab · Jun 14, 2016 · 58f6b45 · 58f6b45
1 parent 57a9c42
commit 58f6b45
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/prob2020/python/permutation.py b/prob2020/python/permutation.py
@@ -13,7 +13,7 @@ def deleterious_permutation(obs_del,
                             num_permutations=10000,
                             stop_criteria=100,
                             pseudo_count=0,
-                            max_batch=1000):
+                            max_batch=25000):
     """Performs null-permutations for deleterious mutation statistics
     in a single gene.
 
@@ -104,7 +104,7 @@ def position_permutation(obs_stat,
                          num_permutations=10000,
                          stop_criteria=100,
                          pseudo_count=0,
-                         max_batch=1000):
+                         max_batch=25000):
     """Performs null-permutations for position-based mutation statistics
     in a single gene.
 

diff --git a/tests/test_deleterious_permutation_test.py b/tests/test_deleterious_permutation_test.py
@@ -71,3 +71,7 @@ def test_100genes_main():
     result = pt.main(opts)
     num_del_sig = np.sum(result['inactivating BH q-value'] < .1)
     assert num_del_sig < 7, 'Few of the 100 test genes should not be significant ({0})'.format(num_del_sig)
+
+
+if __name__ == "__main__":
+    test_100genes_main()