Small fixes

bayespairing/src/draw_single_graph.py

@@ -8,7 +8,7 @@ def draw_graph(g0, title="",node_numbers=False):
     elabels = {}
 
     pos = nx.circular_layout(g0)
-    nodes = nx.draw_networkx_nodes(g0, pos, nodelist=g0.nodes(), node_color='lightgrey', node_size=500, linewidth=2,
+    nodes = nx.draw_networkx_nodes(g0, pos, nodelist=g0.nodes(), node_color='lightgrey', node_size=500, linewidths=2,
                                    alpha=0.99)
     nodes.set_edgecolor("black")
     #for index, i in enumerate(list(g0.nodes(data=True))):

bayespairing/src/make_BN_from_carnaval.py

@@ -45,7 +45,6 @@ def get_pdb_seqs(pdb_list):
 def filter_extra_seqs(seqs):
     good_seqs = []
     for seq in seqs:
-
         if len(seq)<3:
             continue
         seq = "".join(seq)
@@ -251,10 +250,13 @@ def call_makeBN(mod,dataset,left_out, leave_out_seq = False, left_out_seq = "",
     excluded = left_out
     g_list = pickle.load(open("../models/"+dataset + "_one_of_each_graph.cPickle",'rb'))
     seq_list = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))
-    try:
-        motif_seqs  = seq_list[0][mod]
-    except:
-        motif_seqs = seq_list[mod]
+    if type(seq_list) == list:
+        motif_seqs = seq_list[mod][0]
+    else:
+        try:
+            motif_seqs  = seq_list[0][mod]
+        except:
+            motif_seqs = seq_list[mod]
     #print("SEQUENCES",motif_seqs)
 
     #motif_seqs  = pickle.load(open("../models/"+dataset + "_sequences.pickle",'rb'))[0][mod]

bayespairing/test/4GXY.A.1.DESC

 id: 1
-	Bases: 0_G  1_G  2_A  3_A  4_G  20_C 21_A  22_C  23_C  40_G  41_A  42_C  60_G  61_A  62_G  63_A  64_C 
+	Bases: 0_G  1_G  2_A  3_A  4_G  20_C 21_A  22_C  23_C  40_G  41_A  42_C  59_G  60_G  61_A  62_G  63_A  64_C 
 		(    0_G )--- C/C - --- (    1_G )
 		(    1_G )--- C/C - --- (    2_A )
 		(    2_A )--- C/C - --- (    3_A )
@@ -9,6 +9,7 @@ id: 1
 		(   22_C )--- C/C - --- (   23_C )
 		(   40_G )--- C/C - --- (   41_A )
 		(   41_A )--- C/C - --- (   42_C )
+		(   59_G )--- C/C - --- (   60_G )
 		(   60_G )--- C/C - --- (   61_A )
 		(   61_A )--- C/C - --- (   62_G )
 		(   62_G )--- C/C - --- (   63_A )
@@ -16,6 +17,6 @@ id: 1
 		(    0_G )--- +/+ c --- (   64_C )
 		(    4_G )--- +/+ c --- (   20_C )
 		(   23_C )--- +/+ c --- (   40_G )
-		(   42_C )--- +/+ c --- (   60_G )
+		(   42_C )--- +/+ c --- (   59_G )
 		(    3_A )--- 5/5 s --- (   23_C )
 		(    4_G )--- 5/5 s --- (   21_A )
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