def test_prep_sffs_in_dir_no_trim(self):
"""test_prep_sffs_in_dir should use the no_trim option only if sffinfo exists."""
output_dir = tempfile.mkdtemp()
gz_output_dir = tempfile.mkdtemp()
try:
check_sffinfo()
perform_test = True
except:
perform_test = False
if perform_test:
prep_sffs_in_dir(self.sff_dir, output_dir, make_flowgram=False,
convert_to_flx=False, use_sfftools=True,
no_trim=True)
fna_fp = os.path.join(output_dir, 'test.fna')
self.assertEqual(open(fna_fp).read(), fna_notrim_txt)
qual_fp = os.path.join(output_dir, 'test.qual')
self.assertEqual(open(qual_fp).read(), qual_notrim_txt)
self.assertRaises(TypeError, "gzipped SFF", prep_sffs_in_dir,
self.gz_sff_dir, gz_output_dir, make_flowgram=False,
convert_to_flx=False, use_sfftools=True,
no_trim=True)
shutil.rmtree(output_dir)
shutil.rmtree(gz_output_dir)
def test_prep_sffs_in_dir_no_trim(self):
"""test_prep_sffs_in_dir should use the no_trim option only if sffinfo exists."""
output_dir = mkdtemp()
gz_output_dir = mkdtemp()
try:
check_sffinfo()
perform_test = True
except:
perform_test = False
if perform_test:
prep_sffs_in_dir(self.sff_dir,
output_dir,
make_flowgram=False,
convert_to_flx=False,
use_sfftools=True,
no_trim=True)
fna_fp = os.path.join(output_dir, 'test.fna')
self.assertEqual(open(fna_fp).read(), fna_notrim_txt)
qual_fp = os.path.join(output_dir, 'test.qual')
self.assertEqual(open(qual_fp).read(), qual_notrim_txt)
self.assertRaises(TypeError,
"gzipped SFF",
prep_sffs_in_dir,
self.gz_sff_dir,
gz_output_dir,
make_flowgram=False,
convert_to_flx=False,
use_sfftools=True,
no_trim=True)
shutil.rmtree(output_dir)
shutil.rmtree(gz_output_dir)
