# Author: Jonathan Poisson | PoissonJ@ufl.edu 

# !/usr/bin/env python

# Built-in packages
import argparse


# Local packages
from interface import wideToDesign


def getOptions():
    """ Function to pull in arguments """

    description = ""

    parser = argparse.ArgumentParser(description=description)

    group1 = parser.add_argument_group(title='Standard input', description='Standard input for SECIM tools.')
    group1.add_argument("--input", dest="fname", action='store', required=True, help="Input dataset in wide format.")
    group1.add_argument("--design", dest="dname", action='store', required=True, help="Design file.")
    group1.add_argument("--ID", dest="uniqID", action='store', required=True, help="Name of the column with unique identifiers.")
    group1.add_argument("--wideOut", dest="wideOut", action='store', required=True, help="File destination of the cleaned wide file")

    args = parser.parse_args()

    return (args)


def main(args):

    # Import data with clean string as true
    df_cleanedData = wideToDesign(wide=args.fname, design=args.dname,
                                  uniqID=args.uniqID, clean_string=True)

    # Export cleaned data
    df_cleanedData.wide.to_csv(args.wideOut, sep="/t")
    df_cleanedData.design.to_csv(args.designOut, sep="/t")


if __name__ == '__main__':

    # Command line options
    args = getOptions()
    main(args)

@@ -38,17 +38,16 @@
 @ufl.edu
- 
 %0A%0A# !/us
@@ -895,16 +895,156 @@
 e file%22)
+%0A    group1.add_argument(%22--designOut%22, dest=%22designOut%22, action='store', required=True, help=%22File destination of the cleaned design file%22)
 %0A%0A    ar
@@ -1366,25 +1366,25 @@
 deOut, sep=%22
-/
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 t%22)%0A    df_c
@@ -1429,17 +1429,17 @@
 t, sep=%22
-/
+%5C
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Fix clean.py to work with Galaxy