def test_parse_config_with_minimum_elements(self):
with tempfile.NamedTemporaryFile(mode="w") as config:
config.write(
'<?xml version="1.0" encoding="UTF-8"?>'
"<NaspInputData>"
" <Options>"
" <Reference></Reference>"
" <Filters></Filters>"
" </Options>"
" <Files></Files>"
" <ExternalApplications>"
" <Samtools></Samtools>"
" <MatrixGenerator></MatrixGenerator>"
" </ExternalApplications>"
"</NaspInputData>"
)
config.seek(0)
expected = {
"run_name": None,
"output_folder": None,
"reads": [],
"vcfs": [],
"matrix_generator": ("MatrixGenerator", None, "", {}),
"aligners": [],
"reference": (None, None),
"snpcallers": [],
"job_submitter": None,
"alignments": [],
"samtools": ("Samtools", None, "", {}),
"assemblies": [],
"find_dups": None,
}
self.assertDictEqual(expected, configuration_parser.parse_config(config.name))
def test_parse_config_with_minimum_elements(self):
with tempfile.NamedTemporaryFile(mode="w") as config:
config.write('<?xml version="1.0" encoding="UTF-8"?>'
'<NaspInputData>'
' <Options>'
' <Reference></Reference>'
' <Filters></Filters>'
' </Options>'
' <Files></Files>'
' <ExternalApplications>'
' <Samtools></Samtools>'
' <MatrixGenerator></MatrixGenerator>'
' </ExternalApplications>'
'</NaspInputData>')
config.seek(0)
expected = {
'run_name': None,
'output_folder': None,
'reads': [],
'vcfs': [],
'matrix_generator': ('MatrixGenerator', None, '', {}),
'aligners': [],
'reference': (None, None),
'snpcallers': [],
'job_submitter': None,
'alignments': [],
'samtools': ('Samtools', None, '', {}),
'assemblies': [],
'find_dups': None
}
self.assertDictEqual(expected, configuration_parser.parse_config(config.name))
def test_it_reads_the_same_data_it_writes(self):
with TemporaryDirectory(suffix="fjdksnfsdk") as tmpdir:
self.expected["output_folder"] = tmpdir
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, "test_run_name-config.xml"))
self.assertDictEqual(self.expected, observed)
def test_it_reads_the_same_data_it_writes(self):
with TemporaryDirectory(suffix='fjdksnfsdk') as tmpdir:
self.expected['output_folder'] = tmpdir
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, 'test_run_name-config.xml'))
self.assertDictEqual(self.expected, observed)
def test_it_stores_vcfs(self):
with TemporaryDirectory() as tmpdir:
self.expected["output_folder"] = tmpdir
self.expected["vcfs"] = [("foo", "bar")]
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, "test_run_name-config.xml"))
self.assertDictEqual(self.expected, observed)
def test_it_should_warn_when_the_read_element_does_not_contain_read_files(self):
with TemporaryDirectory() as tmpdir:
self.expected["output_folder"] = tmpdir
self.expected["reads"] = [("not_a_valid_read_file", "", "")]
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, "test_run_name-config.xml"))
self.assertDictEqual(self.expected, observed)
def test_it_stores_vcfs(self):
with TemporaryDirectory() as tmpdir:
self.expected['output_folder'] = tmpdir
self.expected['vcfs'] = [
('foo', 'bar')
]
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, 'test_run_name-config.xml'))
self.assertDictEqual(self.expected, observed)
def test_it_should_warn_when_the_read_element_does_not_contain_read_files(self):
with TemporaryDirectory() as tmpdir:
self.expected['output_folder'] = tmpdir
self.expected['reads'] = [
('not_a_valid_read_file', '', '')
]
configuration_parser.write_config(self.expected)
observed = configuration_parser.parse_config(os.path.join(tmpdir, 'test_run_name-config.xml'))
self.assertDictEqual(self.expected, observed)
def main():
import sys
import nasp.dispatcher as dispatcher
import nasp.configuration_parser as configuration_parser
# This is hack to forward commands to gonasp
if len(sys.argv) > 1 and sys.argv[1] in [
'help', 'duplicates', 'frankenfasta', 'matrix', 'export'
]:
if sys.argv[1] == 'help' or any(
arg in ['-h', '-help', '--help']
for arg in sys.argv) or len(sys.argv) < 3:
print(
"Requesting nasp internal command usage message. Enter 'nasp --help' for the nasp pipeline usage message."
)
print(
"Unlike the nasp pipeline, these commands will not be automatically submitted to your job manager"
)
import subprocess
subprocess.call([gonasp_path()] + sys.argv[1:])
return
commandline_args = _parse_args()
if commandline_args.config:
configuration = configuration_parser.parse_config(
commandline_args.config)
output_folder = configuration["output_folder"]
if os.path.exists(output_folder):
response = input(
"\nOutput folder %s already exists!\nFiles in it may be overwritten!\nShould we continue anyway [N]? "
% output_folder)
if not re.match('^[Yy]', response):
print("Operation cancelled!")
quit()
else:
os.makedirs(output_folder)
logfile = os.path.join(output_folder, "runlog.txt")
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)-8s %(message)s',
datefmt='%m/%d/%Y %H:%M:%S',
filename=logfile,
filemode='w')
else:
configuration = _get_user_input(commandline_args.reference_fasta,
commandline_args.output_folder)
configuration_parser.write_config(configuration)
dispatcher.begin(configuration)
def main():
import sys
import nasp.dispatcher as dispatcher
import nasp.configuration_parser as configuration_parser
# This is hack to forward commands to gonasp
if len(sys.argv) > 1 and sys.argv[1] in ['help', 'duplicates', 'frankenfasta', 'matrix', 'export']:
if sys.argv[1] == 'help' or any(arg in ['-h', '-help', '--help'] for arg in sys.argv) or len(sys.argv) < 3:
print("Requesting nasp internal command usage message. Enter 'nasp --help' for the nasp pipeline usage message.")
print("Unlike the nasp pipeline, these commands will not be automatically submitted to your job manager")
import subprocess
subprocess.call([gonasp_path()] + sys.argv[1:])
return
commandline_args = _parse_args()
if commandline_args.config:
configuration = configuration_parser.parse_config(commandline_args.config)
output_folder = configuration["output_folder"]
if os.path.exists(output_folder):
response = input(
"\nOutput folder %s already exists!\nFiles in it may be overwritten!\nShould we continue anyway [N]? " % output_folder)
if not re.match('^[Yy]', response):
print("Operation cancelled!")
quit()
else:
os.makedirs(output_folder)
logfile = os.path.join(output_folder, "runlog.txt")
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)-8s %(message)s',
datefmt='%m/%d/%Y %H:%M:%S',
filename=logfile,
filemode='w')
else:
configuration = _get_user_input(commandline_args.reference_fasta, commandline_args.output_folder)
configuration_parser.write_config(configuration)
dispatcher.begin(configuration)
def main():
import nasp.configuration_parser as configuration_parser
commandline_args = _parse_args()
configuration = configuration_parser.parse_config(commandline_args.config)
begin(configuration)
def main():
import nasp.configuration_parser as configuration_parser
commandline_args = _parse_args()
configuration = configuration_parser.parse_config(commandline_args.config)
begin(configuration)
