From 70dc49e37700bebc5b9c255a84a26efd25dc9e4b Mon Sep 17 00:00:00 2001 From: Tim Lamberton Date: Mon, 3 Aug 2015 15:55:10 +1000 Subject: [PATCH] Fix hard coded bamm executable path in test_bamFilter.py. --- bamm/tests/test_bamFilter.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bamm/tests/test_bamFilter.py b/bamm/tests/test_bamFilter.py index 6019d97..26e3a9f 100644 --- a/bamm/tests/test_bamFilter.py +++ b/bamm/tests/test_bamFilter.py @@ -41,7 +41,7 @@ class TestBamFilter: def setup_class(self): """Setup class variables before any tests.""" - self.bamm = os.path.join("~", "git", "BamM", "bin", "bamm") + #self.bamm = os.path.join("~", "git", "BamM", "bin", "bamm") self.dataDir = os.path.join(os.path.split(__file__)[0], "filter_test_data") self.bamNames = ["1", "2"] @@ -112,8 +112,8 @@ def rmTestFile(self, name): def generate_bam(self, name, args): - cmd = "%s filter -b %s -o %s %s" % (self.bamm, self.bamFiles[name], self.dataDir, " ".join(args)) - subprocess.call(cmd, shell=True) + cmd = "bamm filter -b %s -o %s %s" % (self.bamFiles[name], self.dataDir, " ".join(args)) + subprocess.check_call(cmd, shell=True) def assert_equal_query_sequences(self, out, expected):