"""Replace the name of downloaded GPS assemblies and assembly metadata with the lane ID"""

import glob

import os

import sys

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("--input-dir",

dest="input_dir",

required=True,

help='directory containing files to rename',

type=str)

args = parser.parse_args()

return (args)

def main():

args = get_options()

retieved_files = glob.glob(os.path.join(args.input_dir, "*"))

for file in retieved_files:

dirname = os.path.dirname(file)

newFilename = ".".join(file.split(".")[1:]).split("_")[1:]

newFilename = os.path.join(dirname, "_".join(newFilename[:2]) + "#" + newFilename[2])

if "_additionalAssemblyStats.txt" in file:

newFilename += "_additionalAssemblyStats.txt"

if "_assembly_stats.txt" in file:

newFilename += "_assembly_stats.txt"

os.rename(file, newFilename)

sys.exit(0)

if __name__ == '__main__':

main()