convert_table.py

#!/usr/bin/env python

import argparse
from importlib.metadata import version
from picrust2.util import (check_files_exist, contrib_to_legacy,
                           convert_humann2_to_picrust2,
                           convert_picrust2_to_humann2,
                           convert_picrust2_to_humann2_merged)

CONVERSION_CHOICES = ['contrib_to_legacy',
                      'humann2_strat_to_picrust2',
                      'humann2_unstrat_to_picrust2',
                      'picrust2_unstrat_to_humann2_split',
                      'picrust2_strat_to_humann2_split',
                      'picrust2_to_humann2_merged']

parser = argparse.ArgumentParser(

    description='Converts to and from PICRUSt2 function abundance table. '
    'Currently supports converting to legacy contributional format and to and '
    'from HUMAnN2 function tables. Both stratified and unstratified tables '
    'are supported. Note that the categories like \"UNMAPPED\" in the HUMAnN2 '
    'tables will be removed if they have values of 0. The PICRUSt2 '
    '\"strat\" format refers to the deprecated wide-table stratified table '
    'format only.',

    epilog='''
Usage example:
convert_table.py -o output.tsv -c humann2_strat_to_picrust2 humann2_out/*.tsv
''', formatter_class=argparse.RawDescriptionHelpFormatter)

parser.add_argument('input_files', metavar='INPUT', type=str, nargs='+',
                    help='Input table to convert. If there are multiple input '
                    'files (e.g. if multiple HUMAnN2 gene tables for '
                    'different samples should be converted to a single '
                    'PICRUSt2 table) then specify them all: file1 file2 '
                    'file3...')

parser.add_argument('-o', '--output', metavar='OUTPUT', required=True,
                    type=str,
                    help='Path to output. Corresponds to folder name if '
                         'multiple files are output, otherwise it will be a '
                         'filename.')

parser.add_argument('-c', '--conversion', metavar='CONVERSION', required=True,
                    choices=CONVERSION_CHOICES,
                    help='Type of conversion to perform '
                         '(\'contrib_to_legacy\', '
                         '\'humann2_unstrat_to_picrust2\', '
                         '\'humann2_strat_to_picrust2\', '
                         '\'picrust2_unstrat_to_humann2_split\', '
                         '\'picrust2_strat_to_humann2_split\', or '
                         '\'picrust2_to_humann2_merged\').')

parser.add_argument('--raw_abun', default=False, action='store_true',
                    help='When converting to legacy contributional table '
                         'output abundance (i.e. OTUAbundanceInSample column) '
                         'as raw abundance rather than relative abundances '
                         '(relative abundances are the default).')

parser.add_argument('-v', '--version', default=False, action='version',
                    version="PICRUSt2 " + version('PICRUSt2'))


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)


if __name__ == '__main__':
    main()