def test_main_no_outdir(self):
outfile = 'merged.integrons'
out_dir = os.path.join(self.out_dir, 'real_outdir')
command = 'integron_merge {} {} {}'.format(out_dir, outfile,
' '.join(self.res_dirs))
with self.catch_io(out=True, err=True):
merge.main(command.split()[1:])
# out = sys.stdout.getvalue()
integron_file = os.path.join(out_dir, outfile)
merge.merge_integrons(integron_file, *self.res_dirs)
agg_results = pd.read_csv(integron_file, sep="\t", comment="#")
expe_result_file = self.find_data('acba_lian_pssu_merged.integrons')
expected_results = pd.read_csv(expe_result_file, sep="\t", comment="#")
pdt.assert_frame_equal(agg_results, expected_results)
merge.copy_file(self.out_dir, '.gbk', *self.res_dirs)
merge.copy_file(self.out_dir, '.pdf', *self.res_dirs)
for _id in self.ids:
self.assertTrue(
os.path.exists(os.path.join(out_dir, '{}.gbk'.format(_id))))
self.assertTrue(
os.path.exists(os.path.join(out_dir, '{}_1.pdf'.format(_id))))
def test_merge_integrons(self):
outfile = os.path.join(self.out_dir, 'merged.integrons')
merge.merge_integrons(outfile, *self.res_dirs)
agg_results = pd.read_csv(outfile, sep="\t", comment="#")
expe_result_file = self.find_data('acba_lian_pssu_merged.integrons')
expected_results = pd.read_csv(expe_result_file, sep="\t", comment="#")
pdt.assert_frame_equal(agg_results, expected_results)
def test_merge_integrons(self):
outfile = os.path.join(self.out_dir, 'merged.integrons')
merge.merge_integrons(outfile, *self.res_dirs)
agg_results = pd.read_csv(outfile, sep="\t")
expe_result_file = self.find_data('acba_lian_pssu_merged.integrons')
expected_results = pd.read_csv(expe_result_file, sep="\t")
pdt.assert_frame_equal(agg_results, expected_results)
def test_merge_no_files(self):
outfile = os.path.join(self.out_dir, 'merged.integrons')
for rep, res_dir in zip(self.replicons, self.res_dirs):
os.unlink(os.path.join(res_dir, "{}.integrons".format(rep)))
exp_msg = 'No integrons file to merge'
with self.assertRaises(IntegronError) as ctx:
# 100 is to disable CRITICAL log message
logger_set_level(100)
merge.merge_integrons(outfile, *self.res_dirs)
self.assertEqual(str(ctx.exception), exp_msg)
def test_merge_no_files(self):
outfile = os.path.join(self.out_dir, 'merged.integrons')
for rep, res_dir in zip(self.replicons, self.res_dirs):
os.unlink(os.path.join(res_dir, "{}.integrons".format(rep)))
exp_msg = 'No integrons file to merge'
with self.assertRaises(IntegronError) as ctx:
# 100 is to disable CRITICAL log message
logger_set_level(100)
merge.merge_integrons(outfile, *self.res_dirs)
self.assertEqual(str(ctx.exception), exp_msg)
def test_main(self):
outfile = 'merged.integrons'
command = 'integron_merge {} {} {}'.format(self.out_dir, outfile, ' '.join(self.res_dirs))
with self.catch_io(out=True, err=True):
merge.main(command.split()[1:])
# out = sys.stdout.getvalue()
integron_file = os.path.join(self.out_dir, outfile)
merge.merge_integrons(integron_file, *self.res_dirs)
agg_results = pd.read_csv(integron_file, sep="\t")
expe_result_file = self.find_data('acba_lian_pssu_merged.integrons')
expected_results = pd.read_csv(expe_result_file, sep="\t")
pdt.assert_frame_equal(agg_results, expected_results)
merge.copy_file(self.out_dir, '.gbk', *self.res_dirs)
merge.copy_file(self.out_dir, '.pdf', *self.res_dirs)
for _id in self.ids:
self.assertTrue(os.path.exists(os.path.join(self.out_dir, '{}.gbk'.format(_id))))
self.assertTrue(os.path.exists(os.path.join(self.out_dir, '{}_1.pdf'.format(_id))))