Concatenating csv files using pandas


Mark Isken


May 9, 2016

As part of a research project on hospital capacity planning, I ended up running many computer simulations. For example, there were 150 different scenarios, each requiring 25 runs (replications) of the simulation model. Each run generated a log file that was subsequently processed by a Python script. Much of this post-processing took place in parallel threads with a subset of the scenarios allocated to each thread. After all that, I ended up with a subdirectory containing a number of csv files with identical structure that needed to be combined into one big csv file. Here's a little bit of one of the files.

scenario,rep,timestamp,num_days,num_visits_obs,num_visits_ldr,num_visits_pp, ...
30,1,2016-03-04 12:44:29.610563,105553,42150.0,42154.0,42159.0,8409.0, ...
30,10,2016-03-04 12:48:00.519651,105553,42288.0,42296.0,42305.0,8500.0, ...
30,11,2016-03-04 12:51:30.571655,105553,42210.0,42209.0,42227.0,8387.0, ...
30,12,2016-03-04 12:55:08.550450,105553,42420.0,42433.0,42457.0,8341.0, ...
30,13,2016-03-04 12:58:48.635709,105553,42277.0,42289.0,42301.0,8429.0, ...
30,14,2016-03-04 13:02:21.325709,105553,42127.0,42135.0,42150.0,8581.0, ...
... many more rows and columns

I also wanted to make sure that the final combined file was sorted in ascending order by scenario by replication. Even though I only had a handful of files, manually doing the concatenation using Excel and copying and pasting got old quickly. Also, I often face this same problem but have hundreds of csv files to concatenate. Seemed like a good excuse to put together a Python script to address this problem.


Here is a directory listing of the files to be concatenated.

~/exp9/results_csvs$ ls
results_Exp9_Tandem05_nodischadj_100.csv  results_Exp9_Tandem05_nodischadj_3_5.csv
results_Exp9_Tandem05_nodischadj_1_2.csv  results_Exp9_Tandem05_nodischadj_6_9.csv

The only tricky thing about creating the following Python script was making sure that it worked both on Windows and Linux systems. The backslash vs forward slash issue in file paths can cause grief.

UPDATE 2023 - Use pathlib to make the OS issues go away.

import pandas as pd
import glob
import os

# Inputs
path = './results_csvs/'
stub = 'results_Exp9_Tandem05_nodischadj'
fnpattern = stub + '_*.csv'
sortkeys = ['scenario','rep']

# Create filename pattern to glob that includes the path
# Try to make sure path works in both Windows and Linux

fnpattern_wpath = os.path.normpath(os.path.join(path, fnpattern))

# Create empty dict to hold the DataFrames created as we read each csv file
dfs = {}

# Loop over all the csv files matching our pattern
for csv_fn in glob.glob(fnpattern_wpath):
    # Split the filename off from csv extension. We'll use the filename
    # (without the extension) as the key in the dfs dict.
    fnstub, ext = csv_fn.split('.')

    # Read the next csv file into a pandas DataFrame and add it to
    # the dfs dict.
    df = pd.read_csv(csv_fn)
    dfs[fnstub] = df

# Use pandas concat method to combine the file specific DataFrames into
# one big DataFrame.
bigdf = pd.concat(dfs)

# Since we didn't try to control the order in which the files were read,
# we'll sort the final DataFrame in place by the specified sort keys.
bigdf.sort_values(sortkeys, inplace=True)

# Export the final DataFrame to a csv file. Suppress the pandas index.
bigdf.to_csv(stub + '.csv', index=False)


BibTeX citation:
  author = {Mark Isken},
  title = {Concatenating Csv Files Using Pandas},
  date = {2016-05-09},
  langid = {en}
For attribution, please cite this work as:
Mark Isken. 2016. “Concatenating Csv Files Using Pandas.” May 9, 2016.