def run():
"""
Entry point for the script.
"""
if len(sys.argv) < 2:
sys.argv.append("-h")
plac.call(main)
def router():
"""
Route the tasks based on subcommands parameters.
"""
# Print usage when no parameters are passed.
if len(sys.argv) == 1:
print(USAGE)
sys.exit(1)
# Lowercase the subcommand.
sys.argv[1] = sys.argv[1].lower()
# Check the subcommand.
cmd = sys.argv[1]
# Maintain compatibility with a prior use case (convert == view).
cmd = "convert" if cmd == "view" else cmd
# Raise an error is not a valid subcommand.
if cmd not in SUB_COMMANDS:
print(USAGE, file=sys.stderr)
logger.error(f"invalid command: {cmd}")
sys.exit(-1)
# Remove the command from the list.
sys.argv.remove(cmd)
# Allow multiple forms of parameters to be used.
sys.argv = list(map(proof_reader, sys.argv))
# Delegate to the imported method
modfunc, flag, help = SUB_COMMANDS[cmd]
# Add the help flag if no other information is present beyond command.
if flag and len(sys.argv) == 1:
sys.argv.append("-h")
# Format: module.function
mod_name, func_name = modfunc.rsplit(".", maxsplit=1)
# Dynamic imports to allow other functionality
# to work even when required for certain subcommands may be missing.
mod = importlib.import_module(mod_name)
# Get the function of the module
func = getattr(mod, func_name)
# Execute the function with plac.
plac.call(func)
def run(cmd, capsys, fname=None):
"""
Runs a command and returns its out.
"""
# Ensure the counter starts at zero each time.
jsonrec.reset_counter()
# Drop the leading command (bio)
params = cmd.split()[1:]
# Different functions to be called based on the command.
if params and const.ALIGN_COMMAND in params:
# Run the alignment tests.
params.remove(const.ALIGN_COMMAND)
assert plac.call(align.run, params) is None
elif params and const.TAXON_COMMAND in params:
# Run the alignment tests.
params.remove(const.TAXON_COMMAND)
assert plac.call(taxdb.run, params) is None
elif params and const.DBLINK_COMMAND in params:
# Run the alignment tests.
params.remove(const.DBLINK_COMMAND)
assert plac.call(dblink.run, params) is None
else:
# Run converter commands.
assert plac.call(convert.run, params) is None
# Read the standard out
stream = capsys.readouterr()
result = stream.out
# Check the output if we pass expected value here.
if fname:
expect = read(fname)
if expect != result:
lines1 = expect.splitlines()
lines2 = result.splitlines()
diffs = difflib.unified_diff(lines1, lines2)
print(cmd)
print(f"File: {fname}")
print("-" * 10)
for diff in diffs:
print(diff)
assert result == expect
return result
def router():
"""
Routes the tasks based on incoming parameters.
"""
# Allow multiple forms of parameters to be used.
sys.argv = list(map(proofreader, sys.argv))
# Delayed imports to allow other functionality to work even when some required libraries may be missing.
if const.ALIGN_COMMAND in sys.argv:
# Run alignment related functionality..
sys.argv.remove(const.ALIGN_COMMAND)
from biorun.methods import align
plac.call(align.run)
elif const.TAXON_COMMAND in sys.argv:
# Run taxonomy related functionality.
from biorun.models import taxdb
sys.argv.remove(const.TAXON_COMMAND)
plac.call(taxdb.run)
elif const.DBLINK_COMMAND in sys.argv:
# Run SRA specific functionality.
from biorun.models import dblink
sys.argv.remove(const.DBLINK_COMMAND)
plac.call(dblink.run)
elif const.ONTOLOGY_COMMAND in sys.argv:
# Run SRA specific functionality.
from biorun.models import ontology
sys.argv.remove(const.ONTOLOGY_COMMAND)
plac.call(ontology.run)
else:
# Default action is to convert a file.
from biorun import convert
# Add the help flag if no other information is present.
if len(sys.argv) == 1:
sys.argv.append("-h")
# Delegate parameter parsing to converter.
plac.call(convert.run)
def run():
"""
Entry point for the script.
"""
plac.call(main)
for word in words:
json = fetch.get_json(word)
doubles = [jsonrec.find_taxid(rec) for rec in json] if json else [[]]
taxids = [elem for sublist in doubles for elem in sublist]
if taxids:
terms.extend(taxids)
else:
terms.append(word)
for word in terms:
if lineage:
print_lineage(word, names=names, flat=flat)
else:
query(word, names=names, graph=graph)
# No terms listed. Print database stats.
if not terms:
print_stats(names=names, graph=graph)
if __name__ == '__main__':
# Bony fish: 117565
# Betacoronavirus: 694002
# SARS-COV2: 2697049
# Jawless vertebrates: 1476529
# Vertebrata: 7742
plac.call(run)
def main():
plac.call(run)