poredb_main.py

# Thanks for Andreas Klosterman for dask suggestion
# Thanks to Aaron Quinlan for the argparse implementation from poretools.

import sys
import md5
import hashlib
import re
import argparse
import sqlite3
import version

def run_subtool(parser, args):
	if args.command == 'create':
		import create as submodule
	elif args.command == 'import':
		import importfiles as submodule
	elif args.command == 'fastq':
		import fastq as submodule
	elif args.command == 'updatelengths':
		import updatelengths as submodule
	elif args.command == 'worklist':
		import worklist as submodule
	elif args.command == 'stats':
		import stats as submodule
	elif args.command == 'find':
		import find as submodule

	# run the chosen submodule.
	submodule.run(parser, args)

class ArgumentParserWithDefaults(argparse.ArgumentParser):
	def __init__(self, *args, **kwargs):
		super(ArgumentParserWithDefaults, self).__init__(*args, **kwargs)
		self.add_argument("-q", "--quiet", help="Do not output warnings to stderr",
						  action="store_true",
						  dest="quiet")

def main():
	parser = argparse.ArgumentParser(prog='poredb', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
	parser.add_argument("-v", "--version", help="Installed poretools version",
                        action="version",
                        version="%(prog)s " + str(version.__version__))
	subparsers = parser.add_subparsers(title='[sub-commands]', dest='command', parser_class=ArgumentParserWithDefaults)

	# newdb
	parser_create = subparsers.add_parser('create',
                                          help='Create an empty poredb database')
	parser_create.add_argument('db', metavar='DB',
                             help='The name of the database.')
	parser_create.set_defaults(func=run_subtool)

	# import
	parser_import = subparsers.add_parser('import',
	                                      help='Import files into a poredb database')
	parser_import.add_argument('db', metavar='DB',
	                           help='The poredb database.')
	parser_import.add_argument('fofn', metavar='FOFN',
	                           help='A file containing a list of file names.')
	parser_import.add_argument('--alternate-path', metavar='alternate_path')
	parser_import.set_defaults(func=run_subtool)

	# fastq
	parser_fastq = subparsers.add_parser('fastq',
                                          help='Export basecalls from database in FASTQ format')
	parser_fastq.add_argument('db', metavar='DB',
                             help='The name of the database.')
	parser_fastq.add_argument('-l', '--lengths', dest='report_lengths', default=False, action='store_true', help="Report lengths instead of bases")
	parser_fastq.add_argument('--group-by-asic', default=False, action='store_true', help='Split into one file per asic_id')
	parser_fastq.set_defaults(func=run_subtool)

	# stats
	parser_stats = subparsers.add_parser('stats', help='Show basic summary statistics about database')
	parser_stats.add_argument('db', metavar='DB',
                             help='The name of the database.')
	parser_stats.add_argument('--group-by-asic', default=False, action='store_true', help='Split into one file per asic_id')
	parser_stats.set_defaults(func=run_subtool)

	# worklist
	parser_worklist = subparsers.add_parser('worklist')
	parser_worklist.add_argument('db', metavar='DB',
                             help='The name of the database.')
	parser_worklist.add_argument('fofn', metavar='FOFN',
                                   help='A file containing a list of file names.')
	parser_worklist.set_defaults(func=run_subtool)

	# updatelengths
	parser_updatelengths = subparsers.add_parser('updatelengths', help='')
	parser_updatelengths.add_argument('db', metavar='DB', help='The name of the database.')
	parser_updatelengths.set_defaults(func=run_subtool)

	# findfiles
	parser_find = subparsers.add_parser('find', help='Find path to files by UUID')
	parser_find.add_argument('db', metavar='DB', help='The name of the database.')
	parser_find.add_argument('fofn', metavar='FOFN', help='A file containing a list of UUIDs.')
	parser_find.set_defaults(func=run_subtool)

	args = parser.parse_args()

	if args.quiet:
		logger.setLevel(logging.ERROR)

	args.func(parser, args)

if __name__ == "__main__":
	    main()