Looping Over Data Sets

Overview

Teaching: 5 min
Exercises: 10 min

Questions

• How can I process many data sets with a single command?

Objectives

• Be able to read and write globbing expressions that match sets of files.

• Use glob to create lists of files.

• Write for loops to perform operations on files given their names in a list.

Use a for loop to process files given a list of their names.

• A filename is a character string.
• And lists can contain character strings.

import pandas as pd
for filename in ['data/gapminder_gdp_africa.csv', 'data/gapminder_gdp_asia.csv']:
    data = pd.read_csv(filename, index_col='country')
    print(filename)
    print(data.min())

data/gapminder_gdp_africa.csv gdpPercap_1952    298.846212
gdpPercap_1957    335.997115
gdpPercap_1962    355.203227
gdpPercap_1967    412.977514
⋮ ⋮ ⋮
gdpPercap_1997    312.188423
gdpPercap_2002    241.165877
gdpPercap_2007    277.551859
dtype: float64
data/gapminder_gdp_asia.csv gdpPercap_1952    331
gdpPercap_1957    350
gdpPercap_1962    388
gdpPercap_1967    349
⋮ ⋮ ⋮
gdpPercap_1997    415
gdpPercap_2002    611
gdpPercap_2007    944
dtype: float64

Use glob.glob to find sets of files whose names match a pattern.

• In Unix, the term “globbing” means “matching a set of files with a pattern”.
• The most common patterns are:
  • * meaning “match zero or more characters”
  • ? meaning “match exactly one character”
• Python’s standard library contains the glob module to provide pattern matching functionality
• The glob module contains a function also called glob to match file patterns
• E.g., glob.glob('*.csv') matches all files in the current directory whose names end with .csv.

import glob
print('all csv files in data directory:', glob.glob('data/*.csv'))

all csv files in data directory: ['data/gapminder_all.csv', 'data/gapminder_gdp_africa.csv', \
'data/gapminder_gdp_americas.csv', 'data/gapminder_gdp_asia.csv', 'data/gapminder_gdp_europe.csv', \
'data/gapminder_gdp_oceania.csv']

Use glob and for to process batches of files.

• Helps a lot if the files are named and stored systematically and consistently so that simple patterns will find the right data.

for filename in glob.glob('data/gapminder_*.csv'):
    data = pd.read_csv(filename)
    print(filename, data['gdpPercap_1952'].min())

data/gapminder_all.csv 298.8462121
data/gapminder_gdp_africa.csv 298.8462121
data/gapminder_gdp_americas.csv 1397.717137
data/gapminder_gdp_asia.csv 331.0
data/gapminder_gdp_europe.csv 973.5331948
data/gapminder_gdp_oceania.csv 10039.59564

• This includes all data, as well as per-region data.
• Use a more specific pattern in the exercises to exclude the whole data set.
• But note that the minimum of the entire data set is also the minimum of one of the data sets, which is a nice check on correctness.

Comparing Data

Write a program that reads in the regional data sets and plots the average GDP per capita for each region over time in a single chart.

Solution

import glob
import pandas as pd
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1)
for filename in glob.glob('data/gapminder_gdp*.csv'):
    dataframe = pd.read_csv(filename)
    dataframe.mean().plot(ax=ax, label=filename)
plt.legend()
plt.show()

Key Points

• Use a for loop to process files given a list of their names.

• Use glob.glob to find sets of files whose names match a pattern.

• Use glob and for to process batches of files.