annotate format_metaphlan2_output.py @ 2:370b56f8a02d draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ commit eea46077010e699403ce6995d7d4aac77b2e0b43"

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import argparse


taxo_level_corresp = {
    "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")
    f_n = taxo_level_corresp[level]
    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"),
    }

    for taxo_level_f in taxo_levels_abund_f:
        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:
            s = "kingdom\tphylum\tclass\torder\tfamily\t"
            s += "genus\tspecies\tstrains\tabundance\n"
            output_f.write(s)

            levels_number = 8
            for line in input_f.readlines():
                if line.startswith("#"):
                    continue

                split_line = line[:-1].split("\t")
                all_taxo = split_line[0]
                abundance = split_line[1]

                split_taxo = all_taxo.split("|")
                for level in split_taxo:
                    taxo = level.split("__")[1]
                    taxo = taxo.replace("_", " ")
                    output_f.write(taxo + "\t")

                for i in range(len(split_taxo), levels_number):
                    output_f.write("\t")

                output_f.write(abundance + "\n")

                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)

    for taxo_level_f in taxo_levels_abund_f:
        taxo_levels_abund_f[taxo_level_f].close()


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)
    args = parser.parse_args()

    format_metaphlan2_output(args)