-Fixed #24

PoonLab · Aug 15, 2019 · c24bfb9 · c24bfb9
1 parent 079a07d
commit c24bfb9
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/poplars/common.py b/poplars/common.py
@@ -6,6 +6,15 @@ def convert_fasta(handle):
     """
     result = []
     sequence, h = '', ''
+
+    # Verifies files have correct formatting
+    ln = handle.readline()
+    if ln.startswith('$'):
+        ln = handle.readline()
+    if not (ln.startswith('>') or ln.startswith('#')):
+        print('Invalid FASTA format')
+        raise NameError
+
     for line in handle:
         if line.startswith('$'):  # skip header line
             continue

diff --git a/poplars/tests/test_common.py b/poplars/tests/test_common.py
@@ -2,6 +2,7 @@
 from io import StringIO
 from poplars.common import convert_fasta
 
+
 class TestConvertFasta(unittest.TestCase):
     def testSimpleConversion(self):
         # create file stream as test fixture
@@ -26,5 +27,3 @@ def testMultilineConversion(self):
             ['b', 'GCTAAAAAAAAA']
         ]
         self.assertEqual(expected, result)
-
-