Merge pull request #279 from susannasiebert/reponse_text

respone_text from IEDB is byte not str - handle accordingly

pvacseq/lib/call_iedb.py

@@ -12,11 +12,11 @@
 from subprocess import run, PIPE
 
 def filter_response(response_text):
-    lines = response_text.split("\n")
+    lines = response_text.splitlines()
     remaining_lines = lines.copy()
     for line in lines:
-        if line.startswith("allele"):
-            return "\n".join(remaining_lines)
+        if line.startswith(b"allele"):
+            return b"\n".join(remaining_lines)
         else:
             remaining_lines.pop(0)
 

tests/test_call_iedb.py

@@ -43,10 +43,10 @@ class FilterResponseTests(CallIEDBTests):
     def test_filter_response_ok(self):
         unfiltered_file = os.path.join(self.test_data_dir, 'unfiltered.txt')
         filtered_file   = os.path.join(self.test_data_dir, 'filtered.txt')
-        with open(unfiltered_file, 'r') as f:
-            unfiltered_file_contents = f.read()
-        with open(filtered_file, 'r') as f:
-            filtered_file_contents = f.read()
+        with open(unfiltered_file, 'rb') as f:
+            unfiltered_file_contents = f.read().rstrip()
+        with open(filtered_file, 'rb') as f:
+            filtered_file_contents = f.read().rstrip()
         filtered_response = pvacseq.lib.call_iedb.filter_response(unfiltered_file_contents)
         self.assertEqual(filtered_response, filtered_file_contents)
         filtered_response_on_filtered_file = pvacseq.lib.call_iedb.filter_response(filtered_file_contents)