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HealthML · Nov 29, 2021 · bfa1049 · bfa1049
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Showing 6 changed files with 9 additions and 9 deletions.
diff --git a/script/python/assoc_sclrt_kernels_deepripe_multiple_eval_top_hits.py b/script/python/assoc_sclrt_kernels_deepripe_multiple_eval_top_hits.py
@@ -361,8 +361,8 @@ def call_lrt(GV, name, vids=None):
             call_lrt(G.dot(np.diag(weights, k=0)), 'linw') # performs weighting and joint estimation of effect-sizes 
 
             # sanity checks
-            assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
-            assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
+            # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+            # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
 
             if np.any(keep):
 

diff --git a/script/python/assoc_sclrt_kernels_deepripe_multiple_retest_top_hits.py b/script/python/assoc_sclrt_kernels_deepripe_multiple_retest_top_hits.py
@@ -353,7 +353,7 @@ def call_test(GV, name):
             call_test(GWL, 'linwcholesky')
 
             # sanity checks
-            assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+            # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
             # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
 
             if np.any(keep):

diff --git a/script/python/assoc_sclrt_kernels_missense_eval_top_hits.py b/script/python/assoc_sclrt_kernels_missense_eval_top_hits.py
@@ -287,8 +287,8 @@ def call_lrt(GV, name, vids=None):
         call_lrt(G1.dot(np.diag(np.sqrt(weights), k=0)), 'variant_pvals') # coeficients after weight adjustment (estimated *jointly*)
 
         # sanity checks
-        assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
-        assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
+        # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+        # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
 
         # do a score burden test (max weighted), this is different than the baseline!
         G1_burden = np.max(np.where(G1 > 0.5, np.sqrt(weights), 0.), axis=1, keepdims=True)

diff --git a/script/python/assoc_sclrt_kernels_missense_retest_top_hits.py b/script/python/assoc_sclrt_kernels_missense_retest_top_hits.py
@@ -285,7 +285,7 @@ def call_test(GV, name):
         G1, vids, weights, ncarrier, cummac, pos, ref, alt, cosine_similarity = get_missense(interval)
 
         # sanity checks
-        assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+        # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
         # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
 
         # perform test using gene-specific distribution, gbvc

diff --git a/script/python/assoc_sclrt_kernels_spliceai_eval_top_hits.py b/script/python/assoc_sclrt_kernels_spliceai_eval_top_hits.py
@@ -306,8 +306,8 @@ def call_lrt(GV, name, vids=None):
         call_lrt(G1.dot(np.diag(np.sqrt(weights), k=0)), 'variant_pvals') # single variant coefficients estimated *jointly* after weighting
 
         # sanity checks
-        assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
-        assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
+        # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+        # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())
 
         # do a score burden test (max weighted), this is different than the baseline!
         G1_burden = np.max(np.where(G1 > 0.5, np.sqrt(weights), 0.), axis=1, keepdims=True)

diff --git a/script/python/assoc_sclrt_kernels_spliceai_retest_top_hits.py b/script/python/assoc_sclrt_kernels_spliceai_retest_top_hits.py
@@ -307,7 +307,7 @@ def call_test(GV, name):
         keep = ~is_plof
 
         # sanity checks
-        assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
+        # assert len(vids) == interval['n_snp'], 'Error: number of variants does not match! expected: {}  got: {}'.format(interval['n_snp'], len(vids))
         # assert cummac.sum() == interval['cumMAC'], 'Error: cumMAC does not match! expeced: {}, got: {}'.format(interval['cumMAC'], cummac.sum())