From 0f8ae15d2207d5eaf96066dc4e9e5576973cd5a2 Mon Sep 17 00:00:00 2001
From: Vincent Davis <vincent@vincentdavis.net>
Date: Thu, 3 Dec 2015 19:19:35 -0700
Subject: [PATCH] use with open()

---
 Tests/test_SeqIO_FastaIO.py | 32 +++++++++++++++-----------------
 Tests/test_prosite2.py      | 21 +++++++++------------
 2 files changed, 24 insertions(+), 29 deletions(-)

diff --git a/Tests/test_SeqIO_FastaIO.py b/Tests/test_SeqIO_FastaIO.py
index 20389b96178..e7f1868b629 100644
--- a/Tests/test_SeqIO_FastaIO.py
+++ b/Tests/test_SeqIO_FastaIO.py
@@ -44,29 +44,27 @@ def title_to_ids(title):
 
 def read_single_with_titles(filename, alphabet):
     global title_to_ids
-    handle = open(filename)
-    iterator = FastaIterator(handle, alphabet, title_to_ids)
-    record = next(iterator)
-    try:
-        second = next(iterator)
-    except StopIteration:
-        second = None
-    handle.close()
+    with open(filename) as handle:
+        iterator = FastaIterator(handle, alphabet, title_to_ids)
+        record = next(iterator)
+        try:
+            second = next(iterator)
+        except StopIteration:
+            second = None
     assert record is not None and second is None
     return record
 
 
 def read_title_and_seq(filename):
     """Crude parser that gets the first record from a FASTA file."""
-    handle = open(filename)
-    title = handle.readline().rstrip()
-    assert title.startswith(">")
-    seq = ""
-    for line in handle:
-        if line.startswith(">"):
-            break
-        seq += line.strip()
-    handle.close()
+    with open(filename) as handle:
+        title = handle.readline().rstrip()
+        assert title.startswith(">")
+        seq = ""
+        for line in handle:
+            if line.startswith(">"):
+                break
+            seq += line.strip()
     return title[1:], seq
 
 
diff --git a/Tests/test_prosite2.py b/Tests/test_prosite2.py
index e4b2cd7919d..53be98d2c47 100644
--- a/Tests/test_prosite2.py
+++ b/Tests/test_prosite2.py
@@ -14,11 +14,10 @@
 class TestPrositeRead(unittest.TestCase):
 
     def test_read4(self):
-        "Parsing Prosite record ps00432.txt"
+        """Parsing Prosite record ps00432.txt"""
         filename = os.path.join('Prosite', 'ps00432.txt')
-        handle = open(filename)
-        record = Prosite.read(handle)
-        handle.close()
+        with open(filename) as handle:
+            record = Prosite.read(handle)
         self.assertEqual(record.name, "ACTINS_2")
         self.assertEqual(record.type, "PATTERN")
         self.assertEqual(record.accession, "PS00432")
@@ -453,11 +452,10 @@ def read4_false_etc(self, record):
         self.assertEqual(record.pdb_structs[59], '2BTF')
 
     def test_read5(self):
-        "Parsing Prosite record ps00488.txt"
+        """Parsing Prosite record ps00488.txt"""
         filename = os.path.join('Prosite', 'ps00488.txt')
-        handle = open(filename)
-        record = Prosite.read(handle)
-        handle.close()
+        with open(filename) as handle:
+            record = Prosite.read(handle)
         self.assertEqual(record.name, "PAL_HISTIDASE")
         self.assertEqual(record.type, "PATTERN")
         self.assertEqual(record.accession, "PS00488")
@@ -621,11 +619,10 @@ def test_read5(self):
         self.assertEqual(record.pdb_structs[5], "1Y2M")
 
     def test_read6(self):
-        "Parsing Prosite record ps00546.txt"
+        """Parsing Prosite record ps00546.txt"""
         filename = os.path.join('Prosite', 'ps00546.txt')
-        handle = open(filename)
-        record = Prosite.read(handle)
-        handle.close()
+        with open(filename) as handle:
+            record = Prosite.read(handle)
         self.assertEqual(record.name, "CYSTEINE_SWITCH")
         self.assertEqual(record.type, "PATTERN")
         self.assertEqual(record.accession, "PS00546")