create utility function to call and run WeSME on parameters passed in…

…to compare method

src/dialect/utils/wesme.py

@@ -0,0 +1,24 @@
+import os
+import sys
+
+# TODO: find a cleaner way to import wesme code from external
+current_dir = os.path.dirname(__file__)
+project_root = os.path.abspath(os.path.join(current_dir, "../../../"))
+external_dir = os.path.join(project_root, "external")
+sys.path.append(external_dir)
+
+from WeSME.WeSME import *
+
+
+def run_wesme_analysis(cnt_df, out, interactions):
+    print("Running WeSME analysis...")
+    cnt_df = cnt_df.T  # transpose the count matrix
+    wesme_dout = os.path.join(out, "WeSME_output")
+    os.makedirs(wesme_dout, exist_ok=True)
+    mut_fn = convert_cnt_mtx_to_mut_list(cnt_df, wesme_dout)
+    compute_sample_weights(mut_fn, wesme_dout)
+    freqs_fn = os.path.join(wesme_dout, "sample_mut_freqs.txt")
+    run_weighted_sampling(mut_fn, freqs_fn, 100, wesme_dout, False)
+    gene_pairs = [(ixn.gene_a.name, ixn.gene_b.name) for ixn in interactions]
+    wesme_results_df = compute_pairwise_pvalues(mut_fn, wesme_dout, gene_pairs)
+    return wesme_results_df