"""
import argparse
import anvio
import anvio.tables as t
import anvio.dbops as dbops
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths
run = terminal.Run()
progress = terminal.Progress()
parser = argparse.ArgumentParser(description='A simple script to generate info from search tables')
parser.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db', {'required': False}))
parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': False}))
parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file', {'default': "COLLECTIONS.txt"}))
args = anvio.get_args(parser)
filesnpaths.is_file_exists(args.output_file)
contigs = set([])
contig_lengths = {}
db = dbops.ContigsDatabase(args.contigs_db, quiet=False)
contigs_info_table = db.db.get_table_as_dict(t.contigs_info_table_name)
contig_lengths = dict([(c, contigs_info_table[c]['length']) for c in contigs_info_table])
db.disconnect()
# otherwise update config rule parameters
new_config[param] = default_config[param]
new_config[param].update(config.get(param,''))
else:
# if it's not a dict then it's a general parameter
# update the general parameter
new_config[param] = config.get(param, default_config[param])
filesnpaths.is_output_file_writable(config_path)
open(config_path, 'w').write(json.dumps(new_config, indent=4))
progress.end()
run.info_single("The config file version is now %s. This upgrade brought back any default value that was "
"previously removed from your config file. It will not change anything about the "
"configuration of the resulting workflow and you can just carry on your work. "
"" % (next_version), nl_after=1, nl_before=1, mc='green')
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='A simple script to upgrade a workflow config from version %s to version %s' % (current_version, next_version))
parser.add_argument('config', metavar = 'CONFIG', help = 'Config at version %s' % current_version)
parser.add_argument(*anvio.A("workflow"), **anvio.K("workflow"))
args, unknown = parser.parse_known_args()
try:
migrate(args.config)
except ConfigError as e:
print(e)
sys.exit(-1)
"""
import argparse
import anvio
import anvio.tables as t
import anvio.dbops as dbops
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths
run = terminal.Run()
progress = terminal.Progress()
parser = argparse.ArgumentParser(
description='A simple script to generate info from search tables')
parser.add_argument(*anvio.A('profile-db'),
**anvio.K('profile-db', {'required': False}))
parser.add_argument(*anvio.A('contigs-db'),
**anvio.K('contigs-db', {'required': False}))
parser.add_argument(*anvio.A('output-file'),
**anvio.K('output-file', {'default': "COLLECTIONS.txt"}))
args = parser.parse_args()
filesnpaths.is_file_exists(args.output_file)
contigs = set([])
contig_lengths = {}
db = dbops.ContigsDatabase(args.contigs_db, quiet=False)
contigs_info_table = db.db.get_table_as_dict(t.contigs_info_table_name)