def main_parse_args():
"""Processes command line arguments.
Expects one positional argument (infile) and number of optional
arguments. If arguments are missing, supplies default values.
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('infile',
help='path to the file to be mapped. If mode \
is LIST, it should contain one identifer on each line. \
If mode is EDGE, it should be a single edge file \
produced in table, e.g. biogrid.PPI.edge.1.txt')
parser.add_argument('-mo',
'--mode',
help='mode for running convert. "EDGE" \
if mapping and edge file, or "LIST" to map a list of \
names to the stable ids used in the Knowledge Network',
default='EDGE')
parser.add_argument('-sh',
'--source_hint',
help='suggestion for ID source \
database used to resolve ambiguities in mapping',
default=DEFAULT_HINT)
parser.add_argument('-t',
'--taxon',
help='taxon id of species of all gene \
names',
default=DEFAULT_TAXON)
parser = cf.add_config_args(parser)
args = parser.parse_args()
return args
def main():
"""Parses arguments and then exports the specified subnetworks.
"""
parser = ArgumentParser()
parser = cf.add_config_args(parser)
parser = su.add_config_args(parser)
parser.add_argument("-e", "--edge_type", help="Edge type")
parser.add_argument("-s", "--species", help="Species")
args = parser.parse_args()
db = mu.get_database(args=args)
db.use_db("KnowNet")
cls, bidir = figure_out_class(db, args.edge_type)
edges_fn = '{}.{}.edge'.format(args.species, args.edge_type)
nodes_fn = '{}.{}.node_map'.format(args.species, args.edge_type)
meta_fn = '{}.{}.metadata'.format(args.species, args.edge_type)
bucket_dir = os.path.join(cls, args.species, args.edge_type)
sync_dir = os.path.join(args.bucket, bucket_dir)
sync_edges = os.path.join(sync_dir, edges_fn)
sync_nodes = os.path.join(sync_dir, nodes_fn)
sync_meta = os.path.join(sync_dir, meta_fn)
if not args.force_fetch and all(
map(os.path.exists, [sync_edges, sync_nodes, sync_meta])):
print("Files already exist. Skipping.")
return
get = get_gg if cls == 'Gene' else get_pg
res = get(db, args.edge_type, args.species)
print("ProductionLines: " + str(len(res)))
if not args.force_fetch and should_skip(cls, res):
print('Skipping {}.{}'.format(args.species, args.edge_type))
return
res, lines = norm_edges(res, args)
n1des = list(set(i[0] for i in res))
n2des = list(set(i[1] for i in res))
n1des_desc = convert_nodes(args, n1des)
n2des_desc = convert_nodes(args, n2des)
nodes_desc = set(n1des_desc) | set(n2des_desc)
metadata = get_metadata(db, res, nodes_desc, lines, args.species,
args.edge_type, args)
db.close()
os.makedirs(sync_dir, exist_ok=True)
with open(sync_edges, 'w') as file:
csvw = csv.writer(file, delimiter='\t')
csvw.writerows(res)
with open(sync_nodes, 'w', encoding='utf-8') as file:
csvw = csv.writer(file, delimiter='\t')
csvw.writerows(nodes_desc)
with open(sync_meta, 'w') as file:
yaml.dump(metadata, file, default_flow_style=False)
def main():
"""Deploy a MySQL container using marathon with the provided command line
arguements.
This uses the provided command line arguments and the defaults found in
config_utilities to launch a MySQL docker container using marathon.
"""
parser = ArgumentParser()
parser = cf.add_config_args(parser)
args = parser.parse_args()
deploy_container(args)
def main_parse_args():
"""Processes command line arguments.
Expects three positional arguments(start_step, deploy_loc, run_mode) and
a number of optional arguments. If arguments are missing, supplies default
values.
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('module', help='select SrcClass to check, e.g. dip')
parser = cf.add_config_args(parser)
args = parser.parse_args()
return args
def main_parse_args():
"""Processes command line arguments.
Expects one positional argument (metadata_json) and number of optional
arguments. If arguments are missing, supplies default values.
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('metadata_json',
help='json file produced from check, \
e.g. file_metadata.json')
parser = cf.add_config_args(parser)
args = parser.parse_args()
return args
def main_parse_args():
"""Processes command line arguments.
Expects one positional argument (status_file) and number of optional
arguments. If arguments are missing, supplies default values.
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('importfile',
help='import file produced from map step, \
or merged files, and must contain the table name e.g. \
kegg/ath/kegg.ath.unique.status.1.txt or \
unique.status.txt')
parser = cf.add_config_args(parser)
args = parser.parse_args()
return args
def main_parse_args():
"""Processes command line arguments.
Expects two positional arguments (chunkfile, metadata_json) and number of
optional arguments. If arguments are missing, supplies default values.
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('chunkfile',
help='path to a single chunk file produced \
in fetch, e.g. dip.PPI.raw_line.1.txt')
parser.add_argument('metadata_json',
help='json file produced from check, \
e.g. file_metadata.json')
parser = cf.add_config_args(parser)
args = parser.parse_args()
return args
def main_parse_args():
"""Processes command line arguments.
Expects one argument (start_step) and a number of optional arguments. If
argument is missing, supplies default value.
.. csv-table::
:header: parameter,argument type,flag,description
:widths: 4,2,2,12
:delim: |
[start_step] | | |string indicating which pipeline stage to start with
--setup | |-su |run db inits instead of source specific pipelines
--one_step | |-os |run for a single step instead of rest of pipeline
--step_parameters |str |-p |parameters to specify calls of a single step in pipeline
--no_ensembl | |-ne |do not run ensembl in setup pipeline
--dependencies |str |-d |names of parent jobs that must finish
Returns:
Namespace: args as populated namespace
"""
parser = ArgumentParser()
parser.add_argument('start_step',
default=DEFAULT_START_STEP,
help='start step, must be ' + str(POSSIBLE_STEPS))
parser.add_argument(
'-su',
'--setup',
default=False,
action='store_true',
help='run db inits instead of source specific pipelines')
parser.add_argument('-os',
'--one_step',
default=False,
action='store_true',
help='run for a single step instead of pipeline')
parser.add_argument(
'-p',
'--step_parameters',
default='',
help='parameters to specify calls of a single step in pipeline')
parser.add_argument(
'-ne',
'--no_ensembl',
action='store_true',
default=False,
help='do not run ensembl in setup pipeline',
)
parser.add_argument('-d',
'--dependencies',
default='',
help='names of parent jobs that must finish')
parser = cf.add_config_args(parser)
args = parser.parse_args()
config_opts = sys.argv[1:]
for opt in [
args.start_step, '-p', '--step_parameters', args.step_parameters,
'-d', '--dependencies', args.dependencies
]:
if opt in config_opts:
config_opts.remove(opt)
workflow_opts = []
for opt in ['-su', '--setup', '-os', '--one_step', '-ne', '--no_ensembl']:
if opt in config_opts:
config_opts.remove(opt)
workflow_opts.extend([opt])
args.time_stamp = time.strftime('_%m-%d_%H-%M-%S')
args.config_opts = " ".join(config_opts)
args.workflow_opts = " ".join(workflow_opts)
args.working_dir = args.working_dir.rstrip('/')
args.storage_dir = args.storage_dir.rstrip('/')
return args
