#!/usr/bin/env python3

import sys
sys.path.insert(0, '.')
import argparse
from metatools_ncbi import convert_to_biosample

parser = argparse.ArgumentParser()
parser.add_argument("list_ncbi_ids", type=str,
                    help="text file with a list of NCBI ids that will be converted to biosamples (if possible)")
parser.add_argument("tsv_associations", type=str,
                    help="tsv file with the associations: NCBI id -> biosample (e.g. runid -> biosample)")

if len(sys.argv)==1:
    parser.print_help(sys.stderr)
args = parser.parse_args()

with open(args.list_ncbi_ids, 'r') as inp:
    ncbi_ids = inp.read().splitlines()
list_biosamples=convert_to_biosample.convert_to_biosample(ncbi_ids)
convert_to_biosample.write_tsv(ncbi_ids,list_biosamples,args.tsv_associations)

