quick tips Archives - Python Data

There are times when working with different pandas dataframes that you might need to get the data that is ‘different’ between the two dataframes (i.e.,g Comparing two pandas dataframes and getting the differences). This seems like a straightforward issue, but apparently its still a popular ‘question’ for many people and is my most popular question on stackoverflow.

As an example, let’s look at two pandas dataframes. Both have date indexes and the same structure. How can we compare these two dataframes and find which rows are in dataframe 2 that aren’t in dataframe 1?

dataframe 1 (named df1):

Date       Fruit  Num  Color 
2013-11-24 Banana 22.1 Yellow
2013-11-24 Orange  8.6 Orange
2013-11-24 Apple   7.6 Green
2013-11-24 Celery 10.2 Green

dataframe 2 (named df2):

Date       Fruit  Num  Color 
2013-11-24 Banana 22.1 Yellow
2013-11-24 Orange  8.6 Orange
2013-11-24 Apple   7.6 Green
2013-11-24 Celery 10.2 Green
2013-11-25 Apple  22.1 Red
2013-11-25 Orange  8.6 Orange

The answer, it seems, is quite simple – but I couldn’t figure it out at the time. Thanks to the generosity of stackoverflow users, the answer (or at least an answer that works) is simply to concat the dataframes then perform a group-by via columns and finally re-index to get the unique records based on the index.

Here’s the code (as provided by user alko on stackoverlow):

df = pd.concat([df1, df2]) # concat dataframes
df = df.reset_index(drop=True) # reset the index
df_gpby = df.groupby(list(df.columns)) #group by
idx = [x[0] for x in df_gpby.groups.values() if len(x) == 1] #reindex

This simple approach leads to the correct answer:

        Date   Fruit   Num   Color
9  2013-11-25  Orange   8.6  Orange
8  2013-11-25   Apple  22.1     Red

There are most likely more ‘pythonic’ answers (one suggestion is here) and I’d recommend you dig into those other approaches, but the above works, is easy to read and is fast enough for my needs.

Want more information about pandas for data analysis? Check out the book Python for Data Analysis by the creator of pandas, Wes McKinney.

For years I’ve used the mysql-python library for connecting to mysql databases. It’s worked well for me over the years but there are times when you need speed and/or better connection management that what you get with mysql-python. That’s where SQLAlchemy comes in.

Before diving into this, if you are doing things that aren’t dependent on speed (e.g., it doesn’t matter if it takes 1 second to connect to the database and grab your data and close the database) then you can easily ignore this tip. That said, if you have multiple connections, that connect time can add up.

For example, I recently had an issue where it was taking 4.5+ seconds to connect to a database, run analysis and spit out the results. That’s not terrible if its something for you only but if its a production system and speed is a requirement, that might be too long (and it IS too long).

When I did some analysis using python’s timer() I found that more than 50% of that 4.5 seconds time was in establishing database connections so I grabbed my trusty SQLAlchemy toolkit and went to work.

For those of you that don’t know, SQLAlchemy is a ‘python SQL toolkit and Object Relational Mapper’ (ORM) that is supposed to make things easier when working with SQL databases. For me, the ORM aspect tends to make things more difficult so I tend to stick with plain SQL queries but the SQL toolkit aspect of SQLAlchemy makes a lot of sense and add some time savings when connecting to a SQL database.

Before we get into the SQLAlchemy aspects, let’s take a second to look at how to connect to a SQL database with the mysql-python connector (or at least take a look at how I do it).

First, let’s setup our import statements. For this, we will import MySQLdb, pandas and pandas.io.sql in order to read SQL data directly into a pandas dataframe.

import pandas as pd
import MySQLdb
import pandas.io.sql as psql

Next, let’s create a database connection, create a query, execute that query and close that database.

# setup the database connection.  There's no need to setup cursors with pandas psql.
db=MySQLdb.connect(host=HOST, user=USER, passwd=PW, db=DBNAME)
# create the query
query = "select * from TABLENAME"
# execute the query and assign it to a pandas dataframe
df = psql.read_sql(query, con=db)
# close the database connection
db.close()

This is a fairly standard approach to reading data into a pandas dataframe from mysql using mysql-python. This approach is what I had been using before when I was getting 4.5+ seconds as discussed above. Note – there were multiple database calls and some analysis included in that 4.5+ seconds. A basic database call like the above ran in approximately 0.45 seconds in my code that I was trying to improve performance on and establishing the database connection was the majority of that time.

To improve performance – especially if you will have multiple calls to multiple tables, you can use SQLAlchemy with pandas. You’ll need to pip install sqlalchemy if you don’t have it installed already. Now, let’s setup our imports:

import pandas as pd
import sqlalchemy as sql

Now you can setup your connection string to your database for SQLAlchemy, you’d put everything together like the following:

connect_string = 'mysql://USER:PW@DBHOST/DB'

where USER is your username, PW is your password, DBHOST is the database host and DB is the database you want to connect to.

To setup the persistent connection, you do the following:

sql_engine = sql.create_engine(connect_string)

Now, you have a connection to your database and you’re ready to go. No need to worry about cursors or opening/closing database connections. SQLAlchemy keeps the connection management aspects in for you.

Now all you need to do is focus on your SQL queries and loading the results into a pandas dataframe.

query =query = "select * from TABLENAME"
df = pd.read_sql_query(query, sql_engine)

That’s all it takes. AND…it’s faster. In the example above, my database setup / connection / query / closing times dropped from 0.45 seconds to 0.15 seconds. Times will vary based on what data you are querying and where the database is of course but in this case, all things were the same except for mysql-python being replaced with SQLAlchemy and using the new(ish) read_sql_query function in pandas.

Using this approach, the 4.5+ seconds it took to grab data, analyze the data and return the data was reduced to about 1.5 seconds. Impressive gains for just switching out the connection/management method.

Category: quick tips

Quick Tip: Comparing two pandas dataframes and getting the differences

Quick Tip: SQLAlchemy for MySQL and Pandas