Merge branch 'develop'

flo-compbio · Mar 5, 2017 · 0ca035c · 0ca035c
2 parents 7e92925 + bb95561
commit 0ca035c
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/gopca/go_pca.py b/gopca/go_pca.py
@@ -358,7 +358,8 @@ def _local_filter(params, gse_analysis, enriched, ranked_genes,
                 params.mHG_X_frac, params.mHG_X_min, L,
                 adjust_pval_thresh=False,
                 escore_pval_thresh=params.escore_pval_thresh,
-                gene_set_ids=[gs_id], table=table)
+                gene_set_ids=[gs_id], table=table,
+                exact_pval='if_necessary')
             assert len(enr) in [0, 1]
             # enr will be an empty list if GO term does not meet the p-value
             # threshold
@@ -484,7 +485,8 @@ def _generate_pc_signatures(matrix, params, gse_analysis, W, pc,
             ranked_genes, params.pval_thresh,
             params.mHG_X_frac, params.mHG_X_min, params.mHG_L,
             adjust_pval_thresh=False,
-            escore_pval_thresh=params.escore_pval_thresh)
+            escore_pval_thresh=params.escore_pval_thresh,
+            exact_pval='if_significant')
         if not enriched:
             # no gene sets were found to be enriched
             return []

diff --git a/setup.py b/setup.py
@@ -36,7 +36,7 @@
     'future>= 0.16, <1',
     'unicodecsv>= 0.14.1, <1',
     'xlsxwriter>= 0.7.7, <1',
-    'genometools>=0.2.2, <0.3',
+    'genometools>=0.2.6, <0.3',
     'setuptools>=27.2.0',
 ]
 
@@ -68,7 +68,7 @@
 setup(
     name='gopca',
 
-    version='0.2.1',
+    version='0.2.2',
 
     description=description,
     long_description=long_description,