def test_output_list_starts_with_input(self):
args = [v + '.fq' for v in list('abcd')]
cmd = FastqcCmd(*args)
output = cmd.output()
self.assertEqual(output[:len(args)], args)
def test_output_noninput_items_use_input_directory(self):
args = ['~/tmp/' + v + '.fq' for v in list('abcd')]
cmd = FastqcCmd(*args)
output_html = [o for o in cmd.output() if o.endswith('.html')]
self.assertEqual(
[os.path.dirname(o) for o in output_html],
['~/tmp'] * len(args)
)
def test_output_list_does_not_include_zip_if_extract_flag_set(self):
args = [v + '.fq' for v in list('abcd')]
cmd = FastqcCmd(*args)
cmd.flags.append('--extract')
# REMEMBER: fastqc adds it's own name!
output = [o for o in cmd.output() if o.endswith('.zip')]
self.assertEqual(output, [])
def test_output_list_includes_html_for_each_input(self):
args = [v + '.fq' for v in list('abcd')]
cmd = FastqcCmd(*args)
output_html = [o for o in cmd.output() if o.endswith('.html')]
# REMEMBER: fastqc adds it's own name!
expected = [a.replace('.fq', '_fastqc.html') for a in args]
self.assertEqual(output_html, expected)
def test_output_noninput_items_use_o_flag_directory_when_given(self):
args = ['~/tmp/' + v + '.fq' for v in list('abcd')]
kwargs = {'-o': '~/work'}
cmd = FastqcCmd(*args, **kwargs)
output_html = [o for o in cmd.output() if o.endswith('.html')]
self.assertEqual(
[os.path.dirname(o) for o in output_html],
[kwargs['-o']] * len(args)
)
def test_output_list_includes_zip_for_each_input(self):
args = [v + '.fq' for v in list('abcd')]
cmd = FastqcCmd(*args)
output = [o for o in cmd.output() if o.endswith('.zip')]
# ensure fastqc will not try to extract the data
try:
cmd.flags.remove(['--extract'])
except ValueError:
pass # already gone, no problem
# REMEMBER: fastqc adds it's own name!
expected = [a.replace('.fq', '_fastqc.zip') for a in args]
self.assertEqual(output, expected)
