Fix the bug in issue#120 "NameError: name 'metadata' is not defined"

parasorter/forest_local.py

@@ -497,11 +497,6 @@ def format_nodes(node, node_style, sus_clades, t):
     return supp, sus_clades
 
 
-def parallel_susp_clades(trees):
-    """Parallelizes the function suspicious_clades()"""
-    with Pool(processes=threads) as pool:
-        suspicious = list(pool.map(suspicious_clades, trees))
-        return suspicious
 
 
 def nonredundant(result_clades):
@@ -675,13 +670,19 @@ def backpropagate_contamination(tree_file, cont_names):
         os.mkdir(output_folder)
 
     trees = glob.glob(f"{trees_folder}/*.raxml.support")
+    trees = [os.path.normpath(path).replace('\\', '/') for path in trees]
 
     number_of_genes = len(trees)
     metadata, tax_col = parse_metadata(args.metadata, args.input_metadata)
     threads = args.threads
+    suspicious = []
 
     if not args.backpropagate:
-        suspicious = parallel_susp_clades(trees)
+#        suspicious = parallel_susp_clades(trees)
+        for tree in trees:
+            suspicious.append(suspicious_clades(tree))
+        print(suspicious)
+
         suspicious = sorted(suspicious)
 
         make_txt = False

phylofisher/matrix_constructor.py

@@ -46,9 +46,14 @@ def make_config():
 
 
 def get_output_files():
+    # Accepted out formats with respective suffix
+    out_dict = {'fasta':          'fas',
+                'phylip':         'phy',
+                'phylip-relaxed': 'phy',
+                'nexus':          'nex'}
 
     ret = [
-        f'{args.output}/matrix.fas',
+        f'{args.output}/matrix.{out_dict[args.out_format]}',
         f'{args.output}/indices.tsv',
         f'{args.output}/matrix_constructor_stats.tsv',
         f'{args.output}/occupancy.tsv',
@@ -142,4 +147,4 @@ def run_snakemake(length_filter=False):
     if args.clean_up:
         clean_up()
 
-
+