fix codec error

yachielab · Jan 16, 2019 · 7b3b199 · 7b3b199
1 parent 22a6a36
commit 7b3b199
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/get_spade_annotation.py b/get_spade_annotation.py
@@ -2,14 +2,15 @@
 # -*- coding: utf-8 -*-
 import os
 import sys 
+import codecs
 from Bio import SeqIO
 
 def get_spade_annotations(dir_name = ""):
     dirs = os.listdir(".")
     periodic_repeats = [] 
     spade_gbk_list = [f for f in dirs if "SPADE" in f]  
     for gbk in spade_gbk_list:
-        for record in list(SeqIO.parse(gbk,"genbank")):
+        for record in list(SeqIO.parse(codecs.open(gbk, 'r', 'utf-8', 'ignore'),"genbank")):
             gbk_id   = record.id
             CDS_list = []  
             for feature in record.features: