small updates to makeBN

bayespairing/src/make_BN_from_carnaval.py

@@ -45,12 +45,21 @@ def get_pdb_seqs(pdb_list):
 def filter_extra_seqs(seqs):
     good_seqs = []
     for seq in seqs:
-        if "-" not in seq:
-            good_seqs.append(seq)
+        if len(seq)<3:
+            continue
+        seq = "".join(seq)
+        if "\n" in seq:
+            seq = seq.replace("\n","")
+        if "-" in seq:
+            seq = seq.replace("-","")
+        
+        
+        good_seqs.append(seq)
     return good_seqs
 
 def get_alignment(g,aln,extra_seqs):
     acceptable_extra_seqs = filter_extra_seqs(extra_seqs)
+    #print("processed_extra seqs",acceptable_extra_seqs)
     aln_dict = od()
     nodes = aln.keys()
     snodes = sorted(nodes)
@@ -231,7 +240,12 @@ def call_makeBN(mod,dataset,left_out, leave_out_seq = False, left_out_seq = "",
     current_ID = mod
     excluded = left_out
     g_list = pickle.load(open("../models/"+dataset + "_one_of_each_graph.cPickle",'rb'))
-    motif_seqs  = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))[0][mod]
+    seq_list = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))
+    try:
+        motif_seqs  = seq_list[0][mod]
+    except:
+        motif_seqs = seq_list[mod]
+    #print("SEQUENCES",motif_seqs)
     extra_seqs=[]
     test_seqs = []
     g = g_list[current_ID][0]
@@ -270,8 +284,11 @@ def call_makeBN(mod,dataset,left_out, leave_out_seq = False, left_out_seq = "",
             print("Excluded is not none",excluded)
         if len(indexes)<2:
             indexes = list(range(len(g_list)))
+        try:
+            test_seqs  = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))[1][mod]
+        except:
+            test_seqs = []
         
-        test_seqs  = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))[1][mod]
         if kfold==True:
             excluded_indexes = []
             left_out_index = indexes.index(excluded)