Updated validation code

bayespairing/src/make_BN_from_carnaval.py

@@ -409,31 +409,6 @@ def call_makeBN(mod, dataset, module_data, Lambda=1, Theta=1,retrain=False):
     '''
     
 
-                       
-
-
-
-# Temporary placeholder function for CV for building a Bayesian Network
-def make_BN(module, dataset, graphs, motif_sequences, Lambda=0.35, Theta=1):
-
-    # Test sequences should be tuple of seq and positions, seems like it is outdated/not used
-    test_seqs = []
-
-    # Build the BN with the motif sequences
-    g = graphs[module][0]
-    aln = {}
-    for n in sorted(list(g.nodes())):
-        aln[n] = n
-    alignment = get_alignment(g, aln, motif_sequences)
-
-    motif = make_graph_from_carnaval(g, alignment)
-    pwm = BN_builder.build_pwm(sorted(list(motif.nodes())), alignment)
-
-    BN = BN_builder.build_BN(motif, pwm, alignment)
-
-    # PDBs array is also empty, outdated?
-    BN.from_alignment_dataset(dataset, module, [g], alignment, test_seqs, [], Lambda, Theta)
-    return BN
 
 
 if __name__ == "__main__":

bayespairing/src/module_from_desc.py

@@ -275,13 +275,13 @@ def create_module(desc, fasta, model_name, list_of_nodes, PDBs=[], pdb_info_file
     pdb_aln = []
     pdb_seq = []
     # Try to load PDB_info
-    if os.path.isfile(pdb_info_file):
+    if pdb_info_file is not None and os.path.isfile(pdb_info_file):
         with open(pdb_info_file, 'rb') as f:
             pdb_aln, pdb_seq = pickle.load(f)
 
     # try to load full_seq_file
     full_records = []
-    if os.path.isfile(full_seq_file):
+    if full_seq_file is not None and os.path.isfile(full_seq_file):
         full_records = list(SeqIO.parse(full_seq_file, "fasta"))
 
     # module signatures from list of nodes