def test_call_with_flags(self):
"""Sffinfo flags should alter output as expected."""
# -a flag
a = Sffinfo()
a.Parameters['-a'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, 'FA6P1OK01CGMHQ\n')
# -s flag
a = Sffinfo()
a.Parameters['-s'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ length=48 xy=0892_1356 region=1 '
'run=R_2008_05_28_17_11_38_\n'
'ATCTGAGCTGGGTCATAGCTGCCTCCGTAGGAGGTGCCTCCCTACGGC\n'
)
self.assertEqual(observed, expected)
# -q flag
a = Sffinfo()
a.Parameters['-q'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ length=48 xy=0892_1356 region=1 '
'run=R_2008_05_28_17_11_38_\n'
'32 32 32 32 32 32 32 25 25 21 21 21 28 32 32 31 30 30 32 32 32 '
'33 31 25 18 18 20 18 32 30 28 23 22 22 24 28 18 19 18 16 16 16 '
'17 18 13 17 27 21\n')
self.assertEqual(observed, expected)
# -f flag
a = Sffinfo()
a.Parameters['-f'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ xy=0892_1356 region=1 run=R_2008_05_28_17_11_38_\n'
'A,1.02 C,0.00 G,0.00 T,0.99 A,0.00 C,1.00 G,0.00 T,1.00 A,0.00 C,0.00\n'
'G,1.00 T,0.00 A,1.10 C,0.00 G,1.08 T,0.00 A,0.00 C,1.46 G,0.00 T,0.88\n'
'A,0.18 C,0.00 G,2.69 T,1.01 A,0.08 C,0.96 G,0.00 T,0.02 A,0.92 C,0.08\n'
'G,0.00 T,0.98 A,0.68 C,0.00 G,0.89 T,0.00 A,0.00 C,1.15 G,0.00 T,1.13\n'
'A,0.00 C,0.02 G,1.12 T,0.05 A,0.15 C,1.84 G,0.00 T,1.10 A,0.00 C,2.47\n'
'G,0.96 T,0.86 A,1.06 C,0.00 G,1.96 T,0.12 A,0.93 C,0.13 G,1.65 T,1.06\n'
'A,0.06 C,0.00 G,0.99 T,0.00 A,0.00 C,1.87 G,0.44 T,1.08 A,0.00 C,3.25\n'
'G,0.09 T,0.97 A,0.50 C,1.00 G,1.72 T,0.07 A,0.00 C,0.92 \n')
self.assertEqual(observed, expected)
def test_call_with_accno(self):
"""Sffinfo accession number parameters should filter output."""
# Valid accession number
a = Sffinfo()
a.Parameters['accno'].on('FA6P1OK01CGMHQ')
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, sffinfo_output)
# Invalid accession number
a = Sffinfo()
a.Parameters['accno'].on('AAAAAAAAAAAAAA')
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, empty_sffinfo_output)
def test_input_handler(self):
"""Sffinfo should decorate input handler output with accession numbers"""
my_accno = '12345ABC'
a = Sffinfo()
a.Parameters['accno'].on(my_accno)
self.assertEqual(a.InputHandler, '_input_handler_decorator')
observed = getattr(a, a.InputHandler)(self.sff_fp)
expected = '"%s" %s' % (self.sff_fp, my_accno)
self.assertEqual(observed, expected)
def test_changing_working_dir(self):
"""WorkingDir should be created and included in BaseCommand."""
# Directory is not created, only filename is returned
working_dir = tempfile.mktemp()
self.assertRaises(OSError, os.rmdir, working_dir)
a = Sffinfo(WorkingDir=working_dir)
expected = 'cd "%s/"; sffinfo' % working_dir
self.assertEqual(a.BaseCommand, expected)
# Removing the directory is proof that it was created. If the
# directory is not there, an OSError will be raised.
os.rmdir(working_dir)
def test_base_command(self):
"""BaseCommand should include non-positional parameters."""
s = Sffinfo()
expected = 'cd "%s/"; sffinfo' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
s.Parameters['-a'].on()
expected = 'cd "%s/"; sffinfo -a' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
# accession number parameters should not be included in base command
s.Parameters['-a'].off()
s.Parameters['accno'].on('12345ABC')
expected = 'cd "%s/"; sffinfo' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
def test_call(self):
"""Simple sffinfo call should produce expected output."""
a = Sffinfo()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, sffinfo_output)