#! /usr/bin/python3


import sys
import os
import argparse


def read_params(args):
    parser = argparse.ArgumentParser(description='Convert LEfSe output to '
                                     'Circlader input')
    parser.add_argument('inp_f', metavar='INPUT_FILE', nargs='?',
                        default=None, type=str,
                        help="the input file [stdin if not present]")
    parser.add_argument('out_f', metavar='OUTPUT_FILE', nargs='?',
                        default=None, type=str,
                        help="the output file [stdout if not present]")
    parser.add_argument('-l', metavar='levels with label', default=0, type=int)

    return vars(parser.parse_args())


def lefse2circlader(par):
    finp, fout = bool(par['inp_f']), bool(par['out_f'])

    with open(par['inp_f']) if finp else sys.stdin as inpf:
        put_bm = (l.strip().split('\t') for l in inpf.readlines())
    biomarkers = [p for p in put_bm if len(p) > 2]

    circ = [[b[0],
             "" if b[0].count('.') > par['l'] else b[0].split('.')[-1],
             b[2],
             b[2]+"_col"] for b in biomarkers]

    with open(par['out_f'], 'w') if fout else sys.stdout as out_file:
        for c in circ:
            out_file.write("\t".join(c) + "\n")


if __name__ == '__main__':
    params = read_params(sys.argv)
    lefse2circlader(params)
