From 219991f8fbfc4c09ee24a894ded7e3271765d27a Mon Sep 17 00:00:00 2001
From: Marc Duby <mduby@broadinstitute.org>
Date: Fri, 23 Aug 2024 13:53:12 -0400
Subject: [PATCH] gene_nmf: added ability to set pvalue

---
 app/novelty/gene_nmf/gene_nmf_adapter.py |  8 ++++----
 tests/test_gene_nmf_adapter.py           | 20 ++++++++++++++++++++
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/app/novelty/gene_nmf/gene_nmf_adapter.py b/app/novelty/gene_nmf/gene_nmf_adapter.py
index f3f3de9..7ad263d 100644
--- a/app/novelty/gene_nmf/gene_nmf_adapter.py
+++ b/app/novelty/gene_nmf/gene_nmf_adapter.py
@@ -77,14 +77,14 @@
 
 
 # methods
-def get_gene_nmf_novelty_for_gene_list(list_input_genes, log=False):
+def get_gene_nmf_novelty_for_gene_list(list_input_genes, p_value_cutoff=P_VALUE_CUTOFF, log=False):
     '''
     'will process the gene nmf call for the gene list given and return the gene novelty
     '''
     map_result = {}
 
     # get the calculated data
-    map_gene_novelty, list_input_translated = process_genes(list_input_genes=list_input_genes)
+    map_gene_novelty, list_input_translated = process_genes(list_input_genes=list_input_genes, p_value_cutoff=p_value_cutoff)
 
     # log result
     logger.info("got novelty result map of size: {}".format(len(map_gene_novelty)))
@@ -97,7 +97,7 @@ def get_gene_nmf_novelty_for_gene_list(list_input_genes, log=False):
     return map_result
 
 
-def process_genes(list_input_genes, log=False):
+def process_genes(list_input_genes, p_value_cutoff, log=False):
     '''
     processes the input genes
     '''
@@ -112,7 +112,7 @@ def process_genes(list_input_genes, log=False):
 
     # do the calculations
     list_factor, list_factor_genes, list_factor_gene_sets, gene_factor, gene_set_factor, map_gene_novelty = cutils.calculate_factors(matrix_gene_sets_gene_original=matrix_gene_sets, 
-                                                                                                               p_value=P_VALUE_CUTOFF,
+                                                                                                               p_value=p_value_cutoff,
                                                                                                                list_gene=list_input_translated, 
                                                                                                                list_system_genes=list_system_genes, 
                                                                                                                map_gene_index=map_gene_index, map_gene_set_index=map_gene_set_index,
diff --git a/tests/test_gene_nmf_adapter.py b/tests/test_gene_nmf_adapter.py
index 5cffee8..691ea96 100644
--- a/tests/test_gene_nmf_adapter.py
+++ b/tests/test_gene_nmf_adapter.py
@@ -143,3 +143,23 @@ def test_get_gene_nmf_novelty_for_gene_list():
     assert len(map_result.get('gene_results')) == len(list_gene_test)
 
 
+
+def test_get_gene_nmf_novelty_for_gene_list_and_pvalue():
+    """
+    Test that the gene nmf adaptare novelty function works.
+    """
+    # initialize
+    map_result = {}
+
+    # call method
+    map_result = adapter.get_gene_nmf_novelty_for_gene_list(list_input_genes=list_gene_test, p_value_cutoff=0.2, log=True)
+
+    # logger
+    logger.info("got map result of size: {}".format(len(map_result.get('gene_results'))))
+
+    # test
+    assert map_result is not None
+    assert map_result.get('gene_results') is not None
+    assert len(map_result.get('gene_results')) > 0
+    assert len(map_result.get('gene_results')) == len(list_gene_test)
+