def test_run_metaquast_cmd_list_invalid_num_args(self):
""" test that run_megahit correctly raises a Type Error when an invalid number of arguments is used in place of
required input """
# program path
with self.assertRaises(TypeError):
exec_metaquast.run_metaquast(self.metaquast_path)
def test_run_metaquast_cmd_list_invalid_num_args(self):
""" test that run_megahit correctly raises a Type Error when an invalid number of arguments is used in place of
required input """
# program path
with self.assertRaises(TypeError):
exec_metaquast.run_metaquast(self.metaquast_path)
def test_run_metaquast_icarus_generated(self):
""" test that quast subproccess call generates icarus html report when run_metaquast is passed valid arguments
for the metaquast file path, output directory, and input contigs indicating completion of the
metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
self.assertTrue(os.stat(self.icarus_html).st_size > 0)
def test_run_metaquast_metaquast_log_generated(self):
""" test that quast subproccess call generates metquast log file when run_metaquast is passed valid arguments
for the metaquast file path, output directory, and input contigs indicating that a process has been run and that
input files were modified """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
self.assertTrue(os.stat(self.metaquast_log).st_size>0)
def test_run_metaquast_icarus_generated(self):
""" test that quast subproccess call generates icarus html report when run_metaquast is passed valid arguments
for the metaquast file path, output directory, and input contigs indicating completion of the
metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir,
input_contigs)
self.assertTrue(os.stat(self.icarus_html).st_size > 0)
def test_run_metaquast_metaquast_log_generated(self):
""" test that quast subproccess call generates metquast log file when run_metaquast is passed valid arguments
for the metaquast file path, output directory, and input contigs indicating that a process has been run and that
input files were modified """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir,
input_contigs)
self.assertTrue(os.stat(self.metaquast_log).st_size > 0)
def test_run_metaquast_krona_charts_generated(self):
""" test that quast subproccess call generates krona charts when run_metaquast is passed valid arguments for
the metaquast file path, output directory, and input contigs indicating completion of the metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
# check to see that the krona charts exist
krona_chart_list = os.listdir(self.krona_charts)
self.assertTrue(len(krona_chart_list) > 0)
def test_run_metaquast_krona_charts_generated(self):
""" test that quast subproccess call generates krona charts when run_metaquast is passed valid arguments for
the metaquast file path, output directory, and input contigs indicating completion of the metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir,
input_contigs)
# check to see that the krona charts exist
krona_chart_list = os.listdir(self.krona_charts)
self.assertTrue(len(krona_chart_list) > 0)
def test_run_metaquast_not_aligned_files_generated(self):
""" test that quast subproccess call generates directory containing reports without alignment when
run_metaquast is passed valid arguments for the metaquast file path, output directory, and input contigs
indicating completion of the metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
# check that the not-aligned directory contains files
not_aligned_file_list = os.listdir(self.not_aligned)
self.assertTrue(len(not_aligned_file_list) > 0)
def test_run_metaquast_not_aligned_files_generated(self):
""" test that quast subproccess call generates directory containing reports without alignment when
run_metaquast is passed valid arguments for the metaquast file path, output directory, and input contigs
indicating completion of the metaquast process """
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir,
input_contigs)
# check that the not-aligned directory contains files
not_aligned_file_list = os.listdir(self.not_aligned)
self.assertTrue(len(not_aligned_file_list) > 0)
def test_run_metaquast_cmd_list_no_args(self):
""" test that run_metaquast correctly raises a Value Error when invalid empty string is used in place of
required input """
# arguments to be formatted
null_metaquast_path = ''
# non-existent fasta files
null_fa = []
# option for output directory omitted
null_outdir = None
# catch a value exception when strings are empty
with self.assertRaises(ValueError):
exec_metaquast.run_metaquast(null_metaquast_path, null_outdir, null_fa)
def test_run_metaquast_cmd_list_no_args(self):
""" test that run_metaquast correctly raises a Value Error when invalid empty string is used in place of
required input """
# arguments to be formatted
null_metaquast_path = ''
# non-existent fasta files
null_fa = []
# option for output directory omitted
null_outdir = None
# catch a value exception when strings are empty
with self.assertRaises(ValueError):
exec_metaquast.run_metaquast(null_metaquast_path, null_outdir,
null_fa)
def test_run_metaquast_txt_summary_generated(self):
""" test that quast subproccess call generates directory containing text based summary reports when
run_metaquast is passed valid arguments for the metaquast file path, output directory, and input contigs
indicating completion of the metaquast process """
_TEXT_DIR = "TXT"
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
# check that txt output is available for future pipeline summary
text_summary_dir = os.path.join(self.summary, _TEXT_DIR)
txt_summary_list = os.listdir(text_summary_dir)
self.assertTrue(len(txt_summary_list) > 0)
def test_run_metaquast_txt_summary_generated(self):
""" test that quast subproccess call generates directory containing text based summary reports when
run_metaquast is passed valid arguments for the metaquast file path, output directory, and input contigs
indicating completion of the metaquast process """
_TEXT_DIR = "TXT"
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir,
input_contigs)
# check that txt output is available for future pipeline summary
text_summary_dir = os.path.join(self.summary, _TEXT_DIR)
txt_summary_list = os.listdir(text_summary_dir)
self.assertTrue(len(txt_summary_list) > 0)
def test_run_metaquast_good_stdout(self):
""" test that quast subproccess call reports successful completion message to stdout when run_metaquast
is passed valid arguments for the metaquast file path, output directory, and input contigs """
_SUCCESSFUL_COMPLETION = 'MetaQUAST finished.'
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
stdout, _ = exec_metaquast.run_metaquast(self.metaquast_path, self.output_dir, input_contigs)
# print(stdout)
self.assertNotEqual(stdout.find(_SUCCESSFUL_COMPLETION), -1)
def test_run_metaquast_good_stdout(self):
""" test that quast subproccess call reports successful completion message to stdout when run_metaquast
is passed valid arguments for the metaquast file path, output directory, and input contigs """
_SUCCESSFUL_COMPLETION = 'MetaQUAST finished.'
# input file names
input_contigs = [self.meta_fa_1, self.meta_fa_2]
stdout, _ = exec_metaquast.run_metaquast(self.metaquast_path,
self.output_dir,
input_contigs)
# print(stdout)
self.assertNotEqual(stdout.find(_SUCCESSFUL_COMPLETION), -1)