From 90fbef2b37040d7d39ecb5735ab5bfe528a688cd Mon Sep 17 00:00:00 2001
From: Dillon Barker <dor.barker@gmail.com>
Date: Tue, 24 Sep 2019 11:07:32 -0500
Subject: [PATCH] update subjaln

---
 fsac/update.py | 4 +++-
 test.py        | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/fsac/update.py b/fsac/update.py
index b0bdd9c..cd59bcd 100644
--- a/fsac/update.py
+++ b/fsac/update.py
@@ -114,7 +114,8 @@ def reverse_complement(sequence: str):
             'A': 'T',
             'T': 'A',
             'G': 'C',
-            'C': 'G'
+            'C': 'G',
+            'N': 'N'
             }
 
     return ''.join(complements[x] for x in reversed(sequence))
@@ -136,6 +137,7 @@ def update_genome(genome_data: Dict[str, GeneData],
         if seq is None and name is None:
             continue
 
+        gene['SubjAln'] = seq
         gene['Mismatches'] = 0
         gene['Gaps'] = 0
         gene['QueryName'] = name
diff --git a/test.py b/test.py
index c15cbbf..fd4c287 100644
--- a/test.py
+++ b/test.py
@@ -1,6 +1,6 @@
 import unittest
 
-from src import update
+from fsac import update
 
 class TestUpdate(unittest.TestCase):