Merge pull request #13 from wtsi-npg/devel

Devel

merge_bed.py

@@ -52,7 +52,7 @@ def main():
         if args['prefix']==None: inputPrefix = "."
         else: inputPrefix = args['prefix']
         stemList = pm.findBedStems(inputPrefix)
-    if args['no-validate']==True: validate = False
+    if args['no_validate']==True: validate = False # argparse changes - to _
     else: validate = True
     pm.merge(stemList, args['out'], args['bim'], validate, args['verbose'])
 

plink.py

@@ -817,7 +817,7 @@ def __init__(self):
 
     def plinkAvailable(self):
         """Check that Plink executable is available on PATH"""
-        status = os.system('which plink')
+        status = os.system('which plink > /dev/null')
         if (status!=0): return False
         else: return True
 

test.py

@@ -29,6 +29,7 @@ class TestPlink(unittest.TestCase):
     def setUp(self):
         self.dataDir = '/nfs/gapi/data/genotype/plinktools_test'
         self.outDir = os.path.abspath(mkdtemp(dir='.'))
+        print "Output: "+self.outDir
         self.checksum = ChecksumFinder()
         self.validator = PlinkValidator()
 
@@ -43,6 +44,13 @@ def test_equivalence(self):
         match = pet.compareBinary(stem1, stem3)
         self.assertFalse(match)
 
+    def test_executables(self):
+        """Check that executable scripts compile without crashing"""
+        scripts = ['compare.py', 'het_by_maf.py', 'merge_bed.py']
+        for script in scripts:
+            status = os.system(script+' --help > /dev/null')
+            self.assertEqual(status, 0)
+
     def test_maf_het(self):
         """Test het calculation on high/low maf"""
         stem = os.path.join(self.dataDir, 'samples_part_100_small')