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)