fix python 2 to 3 encoding compatiblity issue

broadinstitute · Oct 29, 2014 · 5fcaa25 · 5fcaa25
1 parent 2edfc49
commit 5fcaa25
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Showing 2 changed files with 39 additions and 37 deletions.
diff --git a/test/test_tools_bwa.py b/test/test_tools_bwa.py
@@ -8,53 +8,55 @@
 
 class TestToolBwa(unittest.TestCase) :
 
-	def setUp(self) :
-		util.file.set_tmpDir('TestToolBwa')
-		self.bwa = tools.bwa.Bwa()
-		self.bwa.install()
+    def setUp(self) :
+        util.file.set_tmpDir('TestToolBwa')
+        self.bwa = tools.bwa.Bwa()
+        self.bwa.install()
 
 
-	def tearDown(self) :
-		util.file.destroy_tmpDir()
+    def tearDown(self) :
+        util.file.destroy_tmpDir()
 
-	def test_tool_bwa_index(self) :
-		referenceDir = util.file.get_test_input_path()
-		expectedDir = util.file.get_test_input_path(self)
+    def test_tool_bwa_index(self) :
+        referenceDir = util.file.get_test_input_path()
+        expectedDir = util.file.get_test_input_path(self)
 
-		fasta = os.path.join(referenceDir, 'ebola.fasta')
-		self.bwa.execute('index', [fasta])
+        fasta = os.path.join(referenceDir, 'ebola.fasta')
+        self.bwa.execute('index', [fasta])
 
-		expected_fasta = os.path.join(expectedDir, 'ebola_expected.fasta')
-		extensions = ['amb', 'ann', 'bwt', 'pac', 'sa']
-		for ext in extensions:
-			result = '{}.{}'.format(fasta, ext)
-			expect = '{}.{}'.format(expected_fasta, ext)
-			self.assertEqual(open(result).read(),
-							open(expect).read())
+        expected_fasta = os.path.join(expectedDir, 'ebola_expected.fasta')
+        extensions = ['amb', 'ann', 'bwt', 'pac', 'sa']
+        for ext in extensions:
+            result = open('{}.{}'.format(fasta, ext), 'rb')
+            expect = open('{}.{}'.format(expected_fasta, ext), 'rb')
 
-	def test_tool_bwa_aln(self) :
-		# referenceDir = util.file.get_test_input_path()
-		expectedDir = util.file.get_test_input_path(self)
+            self.assertEqual(result.read(),
+                             expect.read() )
 
-		# can used expected out for index as input
-		reference = os.path.join(expectedDir, 'ebola_expected.fasta')
-		fastq = os.path.join(expectedDir, 'ebola_aln_input.fastq')
-		output = "{}.sai".format(util.file.mkstempfname())
-		expect = os.path.join(expectedDir, 'ebola_aln_expected.sai')
+            result.close(); expect.close()
 
+    def test_tool_bwa_aln(self) :
+        # referenceDir = util.file.get_test_input_path()
+        expectedDir = util.file.get_test_input_path(self)
 
-		bwa = tools.bwa.Bwa()
-		bwa.install()
+        # can used expected out for index as input
+        reference = os.path.join(expectedDir, 'ebola_expected.fasta')
+        fastq = os.path.join(expectedDir, 'ebola_aln_input.fastq')
+        output = "{}.sai".format(util.file.mkstempfname())
+        expect = os.path.join(expectedDir, 'ebola_aln_expected.sai')
 
-		bwa.execute('aln', [reference, fastq], options={'-q': 5, '-t': 4},
-				post_cmd=" > {}".format(output))
 
-		self.assertEqual(open(output).read(),
-							open(expect).read())
-		# extensions = ['amb', 'ann', 'bwt', 'pac', 'sa']
-		# for ext in extensions:
-			# result = '{}.{}'.format(fasta, ext)
-			# expect = '{}.{}'.format(expected_fasta, ext)
+        bwa = tools.bwa.Bwa()
+        bwa.install()
+
+        bwa.execute('aln', [reference, fastq], options={'-q': 5, '-t': 4},
+                post_cmd=" > {}".format(output))
+
+        result = open(output, 'rb')
+        gold = open(expect, 'rb')
+        self.assertEqual(result.read(),
+                         gold.read())
+        result.close(); gold.close()
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/tools/bwa.py b/tools/bwa.py
@@ -53,7 +53,7 @@ def execute(self, subcommand, args=[], options={}, option_string="",
 		"""
 		arg_str = " ".join(args)
 		option_str = '{} {}'.format(' '.join([ "{} {}".format(k, v) for k, v in
-												options.iteritems() ]),
+												options.items() ]),
 									option_string
 									)
 		cmd =  "{self.exec_path} {subcommand} {option_str} {arg_str} {post_cmd}" \