From 58f6b454bc6122568dafbfe82db2d47ee76d0aa6 Mon Sep 17 00:00:00 2001 From: ctokheim Date: Tue, 14 Jun 2016 10:37:07 -0400 Subject: [PATCH] Updated memory handling --- prob2020/python/permutation.py | 4 ++-- tests/test_deleterious_permutation_test.py | 4 ++++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/prob2020/python/permutation.py b/prob2020/python/permutation.py index c8df7e4..66bdced 100644 --- 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 index dd58f9b..2a6aa27 100644 --- 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()