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SortColNames
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SortColNames
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#!/usr/bin/env python3
# This is the sixth script in the PopMLST pipeline. Run it
# without arguments to get the usage. Please provide
# proper attribution if you use this code.
#
# https://github.com/marade/PopMLST
#
# author: M Radey (email: marad_at_uw.edu)
import os, sys, argparse
import pandas as pd
from colorama import init as cinit
from colorama import Fore, Back, Style
cinit(autoreset=True)
version = "1.0.0"
def do_args():
desc = "Rearrange columns in a tab delimited file in alphabetical order"
parser = argparse.ArgumentParser(prog=os.path.basename(__file__),\
description=desc)
parser.add_argument("infile", help="specifies the input file")
parser.add_argument("outfile", help="specifies the output file")
return parser.parse_args()
def reorder_columns(infile, outfile):
print(Fore.CYAN + Style.BRIGHT + "Sorting columns...")
df = pd.read_csv(infile, sep='\t', index_col=0)
df = df.reindex(sorted(df.columns), axis=1)
df.to_csv(outfile, sep='\t')
def main():
# setup
args = do_args()
args.outfile = os.path.abspath(args.outfile)
args.infile = os.path.abspath(args.infile)
reorder_columns(args.infile, args.outfile)
print(Fore.CYAN + Style.BRIGHT + "Done.")
return 0
if __name__ == "__main__":
sys.exit(main())