Merge pull request #173 from bowenliu16/master

"""

Manipulate CSV data files.

"""

from __future__ import print_function

from __future__ import division

from __future__ import absolute_import

import pandas as pd

import csv

import argparse

def parse_args(input_args=None):

  parser = argparse.ArgumentParser()

  parser.add_argument(

    "--descriptor", required=1,

    help="Name of input descriptor CSV file.")

  parser.add_argument(

    "--activities", required=1,

    help="Name of input activities CSV file.")

  parser.add_argument(

    "--output", required=1,

    help="Name of output CSV file.")

  return parser.parse_args(input_args)

def remove_trailing_comma(infile, outfile):

  with open(infile, 'r') as infile, open(outfile, 'w') as outfile:

    csv_writer = csv.writer(outfile)

    for row in csv.reader(infile):

      csv_writer.writerow(row[:-1])  # removes the last comma in each row

# TODO (Bowen): make this function less memory intensive

def combine_descriptor_activities(descriptor_file, activities_file, outfile):

  # set 1st column as the column index of dataframe

  descriptor_df = pd.read_csv(descriptor_file,

                              index_col=0)

  activities_df = pd.read_csv(activities_file, index_col=0)

  # merge descriptor and activities dataframe into output dataframe based on

  # the molecule name, which is the index for both dataframes (but named

  # differently). Default merge is inner merge

  combined_df = pd.merge(descriptor_df, activities_df,

                         left_index=True, right_index=True)

  # need to manually set dataframe indexname after merge based on index

  combined_df.index.name = "Molecule"

  combined_df.to_csv(outfile)

def main():

  args = parse_args()

  descriptor_file = args.descriptor

  activities_file = args.activities

  outfile = args.output

  combine_descriptor_activities(descriptor_file, activities_file, outfile)

if __name__ == '__main__':

  main()