def main(argv=None):
"""Run **isatools** from the command line
Arguments
argv (list, optional): the list of arguments to run isatools
with (if None, then sys.argv is used) [default: None]
"""
p = argparse.ArgumentParser(
prog=__name__,
formatter_class=argparse.RawDescriptionHelpFormatter,
description=
'''Create, convert, and manipulate ISA-formatted metadata''',
usage='isatools -c COMMAND [options]',
)
p.add_argument('-c',
dest='cmd',
help='isatools API command to run',
required=True,
choices=[
'isatab2json', 'json2isatab', 'sampletab2isatab',
'sampletab2json'
])
p.add_argument('-i',
dest='in_path',
help='in (files or directory will be read from here)',
required=True)
p.add_argument(
'-o',
dest='out_path',
help=
'out (file will be written out here or written to directory if ISA-Tab '
'archive out)',
required=True)
p.add_argument('--version',
action='version',
version='isatools {}'.format("0.7"))
p.add_argument('-v',
dest='verbose',
help="show more output",
action='store_true',
default=False)
args = p.parse_args(argv or sys.argv[1:])
if args.verbose:
print("{} input: {}".format(os.linesep, args.in_path))
print("output: {}".format(args.out_path))
if args.cmd == 'isatab2json':
from isatools.convert import isatab2json
J = isatab2json.convert(args.in_path)
with open(args.out_path, 'w') as out_fp:
json.dump(J, out_fp)
elif args.cmd == 'json2isatab':
from isatools.convert import json2isatab
with open(args.in_path) as in_fp:
json2isatab.convert(in_fp, args.out_path)
elif args.cmd == 'sampletab2isatab':
from isatools.convert import sampletab2isatab
with open(args.in_path) as in_fp:
sampletab2isatab.convert(in_fp, args.out_path)
elif args.cmd == 'sampletab2json':
from isatools.convert import sampletab2json
with open(args.in_path) as in_fp:
with open(args.out_path, 'w') as out_fp:
sampletab2json.convert(in_fp, out_fp)
def test_sampletab2json_GSB_718(self):
with open(os.path.join(self._sampletab_dir,
"GSB-718.txt")) as sampletab_fp:
sampletab2isatab.convert(source_sampletab_fp=sampletab_fp,
target_dir=self._tmp_dir)
