_module_path, _module_name = os.path.split(__file__)
sys.path.append(os.path.join(_module_path, '..', 'scripts'))
-import srf2named_fastq
+from htsworkflow.pipelines import srf2fastq
class testSrf2Fastq(unittest.TestCase):
def test_split_good(self):
target1 = StringIO()
target2 = StringIO()
- srf2named_fastq.convert_single_to_two_fastq(source, target1, target2)
+ srf2fastq.convert_single_to_two_fastq(source, target1, target2)
target1.seek(0)
lines1 = target1.readlines()
target1 = StringIO()
target2 = StringIO()
- srf2named_fastq.convert_single_to_two_fastq(source, target1, target2, header="foo_")
+ srf2fastq.convert_single_to_two_fastq(source, target1, target2, header="foo_")
target1.seek(0)
lines1 = target1.readlines()
""")
target1 = StringIO()
- srf2named_fastq.convert_single_to_fastq(source, target1)
+ srf2fastq.convert_single_to_fastq(source, target1)
target1.seek(0)
lines1 = target1.readlines()
""")
target1 = StringIO()
- srf2named_fastq.convert_single_to_fastq(source, target1, header="foo_")
+ srf2fastq.convert_single_to_fastq(source, target1, header="foo_")
target1.seek(0)
lines1 = target1.readlines()
cnf1_srf = 'woldlab_090512_HWI-EAS229_0114_428NNAAXX_5.srf'
cnf1_path = os.path.join(_module_path, cnf1_srf)
- is_srf = srf2named_fastq.is_srf
+ is_srf = srf2fastq.is_srf
self.failUnlessEqual(is_srf(__file__), False)
self.failUnlessEqual(is_srf(cnf4_path), True)
self.failUnlessEqual(is_srf(cnf1_path), True)
cnf1_srf = 'woldlab_090512_HWI-EAS229_0114_428NNAAXX_5.srf'
cnf1_path = os.path.join(_module_path, cnf1_srf)
- is_cnf1 = srf2named_fastq.is_cnf1
+ is_cnf1 = srf2fastq.is_cnf1
self.failUnlessRaises(ValueError, is_cnf1, __file__)
self.failUnlessEqual(is_cnf1(cnf4_path), False)
self.failUnlessEqual(is_cnf1(cnf1_path), True)