def main():
args = parser.parse_args()
# Check that input files exist.
check_files_exist(args.input_files)
if args.conversion == 'contrib_to_legacy':
if args.raw_abun:
rel_abun_set = False
else:
rel_abun_set = True
contrib_to_legacy(args.input_files, args.output, rel_abun_set)
elif args.conversion == 'humann2_unstrat_to_picrust2':
convert_humann2_to_picrust2(args.input_files, args.output, False)
elif args.conversion == 'humann2_strat_to_picrust2':
convert_humann2_to_picrust2(args.input_files, args.output, True)
elif args.conversion == 'picrust2_unstrat_to_humann2_split':
convert_picrust2_to_humann2(args.input_files, args.output, False)
elif args.conversion == 'picrust2_strat_to_humann2_split':
convert_picrust2_to_humann2(args.input_files, args.output, True)
elif args.conversion == 'picrust2_to_humann2_merged':
convert_picrust2_to_humann2_merged(args.input_files, args.output)
def test_humann2_strat_to_picrust2(self):
with TemporaryDirectory() as temp_dir:
outfile = path.join(temp_dir, "test_out")
convert_humann2_to_picrust2([humann2_strat_in], outfile, True)
obs_out = pd.read_table(outfile, sep="\t", index_col=[0, 1])
exp_out = pd.read_table(humann2_strat_exp, sep="\t", index_col=[0, 1])
pd.testing.assert_frame_equal(obs_out, exp_out, check_like=True)
def main():
args = parser.parse_args()
# Check that input files exist.
check_files_exist(args.input_files)
if args.conversion == 'humann2_unstrat_to_picrust2':
convert_humann2_to_picrust2(args.input_files, args.output, False)
elif args.conversion == 'humann2_strat_to_picrust2':
convert_humann2_to_picrust2(args.input_files, args.output, True)
elif args.conversion == 'picrust2_unstrat_to_humann2_split':
convert_picrust2_to_humann2(args.input_files, args.output, False)
elif args.conversion == 'picrust2_strat_to_humann2_split':
convert_picrust2_to_humann2(args.input_files, args.output, True)
elif args.conversion == 'picrust2_to_humann2_merged':
convert_picrust2_to_humann2_merged(args.input_files, args.output)