import json

import sys

from tqdm import tqdm

def get_options():

import argparse

description = 'Download reads of interest by accession ID'

parser = argparse.ArgumentParser(description=description,

prog='extract_entrez_reads')

io_opts = parser.add_argument_group('input')

io_opts.add_argument("--file",

dest="input",

required=True,

help='txt file listing isolate biosamples and EBI assembly paths (http://ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k/)',

type=str)

args = parser.parse_args()

return (args)

def main():

"""Main function. Parses command line args and calls functions."""

args = get_options()

with open(args.input, "r") as inFile:

assembly_list = inFile.read().splitlines()

assembly_link_dict = {}

for line in tqdm(assembly_list):

split = line.split("\t")

biosample = split[0]

assemblyURL = split[1].replace("/ebi/ftp/", "http://ftp.ebi.ac.uk/")

assembly_link_dict[biosample] = assemblyURL

with open("661K_biosampleAssemblyURLs.json", "w") as keyFile:

keyFile.write(json.dumps(assembly_link_dict))

sys.exit(0)

if __name__ == '__main__':

main()