| Previous changeset 1:1e74cb2c8e67 (2020-09-14) Next changeset 3:2c87f56bd53a (2023-11-04) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43" |
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modified:
format_metaphlan2_output.py |
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| diff -r 1e74cb2c8e67 -r 370b56f8a02d format_metaphlan2_output.py --- a/format_metaphlan2_output.py Mon Sep 14 09:52:15 2020 +0000 +++ b/format_metaphlan2_output.py Wed Oct 19 14:39:16 2022 +0000 |
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| @@ -5,42 +5,43 @@ taxo_level_corresp = { - 'k': 'kingdom', - 'p': 'phylum', - 'c': 'class', - 'o': 'order', - 'f': 'family', - 'g': 'genus', - 's': 'species', - 't': 'strains'} - + "k": "kingdom", + "p": "phylum", + "c": "class", + "o": "order", + "f": "family", + "g": "genus", + "s": "species", + "t": "strains", +} + def write_taxo_abundance(output_files, level, taxo, abundance): if level not in taxo_level_corresp: - raise ValueError(level + ' is not a know taxonomic level') + raise ValueError(level + " is not a know taxonomic level") f_n = taxo_level_corresp[level] - output_files[f_n].write(taxo + '\t') - output_files[f_n].write(abundance + '\n') + output_files[f_n].write(taxo + "\t") + output_files[f_n].write(abundance + "\n") def format_metaphlan2_output(args): taxo_levels_abund_f = { - 'kingdom': open(args.kingdom_abundance_file, 'w'), - 'phylum': open(args.phylum_abundance_file, 'w'), - 'class': open(args.class_abundance_file, 'w'), - 'order': open(args.order_abundance_file, 'w'), - 'family': open(args.family_abundance_file, 'w'), - 'genus': open(args.genus_abundance_file, 'w'), - 'species': open(args.species_abundance_file, 'w'), - 'strains': open(args.strains_abundance_file, 'w') + "kingdom": open(args.kingdom_abundance_file, "w"), + "phylum": open(args.phylum_abundance_file, "w"), + "class": open(args.class_abundance_file, "w"), + "order": open(args.order_abundance_file, "w"), + "family": open(args.family_abundance_file, "w"), + "genus": open(args.genus_abundance_file, "w"), + "species": open(args.species_abundance_file, "w"), + "strains": open(args.strains_abundance_file, "w"), } for taxo_level_f in taxo_levels_abund_f: - s = taxo_level_f + '\t' + 'abundance\n' + s = taxo_level_f + "\t" + "abundance\n" taxo_levels_abund_f[taxo_level_f].write(s) - with open(args.metaphlan2_output, 'r') as input_f: - with open(args.all_taxo_level_abundance_file, 'w') as output_f: + with open(args.metaphlan2_output, "r") as input_f: + with open(args.all_taxo_level_abundance_file, "w") as output_f: s = "kingdom\tphylum\tclass\torder\tfamily\t" s += "genus\tspecies\tstrains\tabundance\n" output_f.write(s) @@ -50,46 +51,42 @@ if line.startswith("#"): continue - split_line = line[:-1].split('\t') + split_line = line[:-1].split("\t") all_taxo = split_line[0] abundance = split_line[1] - split_taxo = all_taxo.split('|') + split_taxo = all_taxo.split("|") for level in split_taxo: - taxo = level.split('__')[1] + taxo = level.split("__")[1] taxo = taxo.replace("_", " ") - output_f.write(taxo + '\t') + output_f.write(taxo + "\t") for i in range(len(split_taxo), levels_number): - output_f.write('\t') + output_f.write("\t") output_f.write(abundance + "\n") - last_taxo_level = split_taxo[-1].split('__') + last_taxo_level = split_taxo[-1].split("__") taxo = last_taxo_level[1].replace("_", " ") level = last_taxo_level[0] - write_taxo_abundance( - taxo_levels_abund_f, - level, - taxo, - abundance) + write_taxo_abundance(taxo_levels_abund_f, level, taxo, abundance) for taxo_level_f in taxo_levels_abund_f: taxo_levels_abund_f[taxo_level_f].close() -if __name__ == '__main__': +if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('--metaphlan2_output', required=True) - parser.add_argument('--all_taxo_level_abundance_file', required=True) - parser.add_argument('--kingdom_abundance_file', required=True) - parser.add_argument('--phylum_abundance_file', required=True) - parser.add_argument('--class_abundance_file', required=True) - parser.add_argument('--order_abundance_file', required=True) - parser.add_argument('--family_abundance_file', required=True) - parser.add_argument('--genus_abundance_file', required=True) - parser.add_argument('--species_abundance_file', required=True) - parser.add_argument('--strains_abundance_file', required=True) + parser.add_argument("--metaphlan2_output", required=True) + parser.add_argument("--all_taxo_level_abundance_file", required=True) + parser.add_argument("--kingdom_abundance_file", required=True) + parser.add_argument("--phylum_abundance_file", required=True) + parser.add_argument("--class_abundance_file", required=True) + parser.add_argument("--order_abundance_file", required=True) + parser.add_argument("--family_abundance_file", required=True) + parser.add_argument("--genus_abundance_file", required=True) + parser.add_argument("--species_abundance_file", required=True) + parser.add_argument("--strains_abundance_file", required=True) args = parser.parse_args() format_metaphlan2_output(args) |