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#!/usr/bin/env python3
"""
SeQuencing Tools -- command-line tools for working with sequencing data
"""
__author__ = "Marcel Martin"
import logging
import importlib
from . import HelpfulArgumentParser
from . import __version__
from .commands import fastxmod
logger = logging.getLogger(__name__)
# List of all subcommands. A module of the given name must exist and define
# add_arguments() and main() functions. Documentation is taken from the first
# line of the module’s docstring.
COMMANDS = [
'align',
'bam2fastq',
'fastxmod',
'qgramfreq',
'chars',
'fastagrep',
'readcov',
'randomseq',
'samsetop',
'bameof',
'readlenhisto',
'cutvect',
]
def main():
logging.basicConfig(level=logging.INFO, format='%(levelname)s: %(message)s')
parser = HelpfulArgumentParser(description=__doc__, prog='sqt')
parser.add_argument('--version', action='version', version='%(prog)s ' + __version__)
subparsers = parser.add_subparsers()
for command_name in COMMANDS:
module = importlib.import_module('.commands.' + command_name, 'sqt')
subparser = subparsers.add_parser(command_name,
help=module.__doc__.split('\n')[1], description=module.__doc__)
subparser.set_defaults(func=module.main)
module.add_arguments(subparser)
args = parser.parse_args()
if not hasattr(args, 'func'):
parser.error("Please provide a command")
else:
args.func(args)
if __name__ == '__main__':
main()
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