"""
The top-level augur command which dispatches to subcommands.
"""
import argparse
import re
import os
import sys
import importlib
from types import SimpleNamespace
from .utils import first_line
recursion_limit = os.environ.get("AUGUR_RECURSION_LIMIT")
if recursion_limit:
sys.setrecursionlimit(int(recursion_limit))
command_strings = [
"parse",
"filter",
"mask",
"align",
"tree",
"refine",
"ancestral",
"translate",
"reconstruct_sequences",
"clades",
"traits",
"sequence_traits",
"lbi",
"distance",
"titers",
"frequencies",
"export",
"validate",
"version",
"import"
]
COMMANDS = [importlib.import_module('augur.' + c) for c in command_strings]
def make_parser():
parser = argparse.ArgumentParser(
prog = "augur",
description = "Augur: A bioinformatics toolkit for phylogenetic analysis.")
subparsers = parser.add_subparsers()
add_default_command(parser)
add_version_alias(parser)
for command in COMMANDS:
# Add a subparser for each command.
subparser = subparsers.add_parser(
command_name(command),
help = first_line(command.__doc__),
description = command.__doc__)
subparser.set_defaults(__command__ = command)
# Let the command register arguments on its subparser.
command.register_arguments(subparser)
# Use the same formatting class for every command for consistency.
# Set here to avoid repeating it in every command's register_parser().
subparser.formatter_class = argparse.ArgumentDefaultsHelpFormatter
return parser
def run(argv):
args = make_parser().parse_args(argv)
try:
return args.__command__.run(args)
except RecursionError:
print("FATAL: Maximum recursion depth reached. You can set the env variable AUGUR_RECURSION_LIMIT to adjust this (current limit: {})".format(sys.getrecursionlimit()))
sys.exit(2)
def add_default_command(parser):
"""
Sets the default command to run when none is provided.
"""
class default_command():
def run(args):
parser.print_help()
return 2
parser.set_defaults(__command__ = default_command)
def add_version_alias(parser):
"""
Add --version as a (hidden) alias for the version command.
It's not uncommon to blindly run a command with --version as the sole
argument, so its useful to make that Just Work.
"""
class run_version_command(argparse.Action):
def __call__(self, *args, **kwargs):
opts = SimpleNamespace()
sys.exit( version.run(opts) )
return parser.add_argument(
"--version",
nargs = 0,
help = argparse.SUPPRESS,
action = run_version_command)
def command_name(command):
"""
Returns a short name for a command module.
"""
def remove_prefix(prefix, string):
return re.sub('^' + re.escape(prefix), '', string)
package = command.__package__
module_name = command.__name__
return remove_prefix(package, module_name).lstrip(".").replace("_", "-")
