Python Fundamentals

Overview

Questions

• What basic data types can I work with in Python?
• How can I create a new variable in Python?
• How do I use a function?
• Can I change the value associated with a variable after I create it?

Objectives

• Assign values to variables.

Before we begin

Open the collaborative doc for our workshop https://broad.io/cb-python-20240624

You’ll find all the links listed below in the collaborative doc.

If you haven’t completed your workshop setup please visit https://broad.io/cb-python-setup

If you need help with setup, please put the pink post-it on your computer and a TA will come help you.

If you’ve created your colab account, downloaded the workshop data files, uploaded it to your colab account’s google drive AND successfully run the access test, please put the green post-it on your computer to indicate your setup is complete.

To run the access test, visit https://broad.io/cb-python-access-test, 1. click “Copy to Drive” and, in YOUR COPY of Python_workshop_data_access_test.ipynb 2. click the ▶️ symbol on the left hand side of the cell.

This is what success looks like:

Feel free to browse today’s lesson content https:/broad.io/cb-python-20240624-lesson

Google colab

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Google colab is a web-based computational notebook hosted in the cloud by Google. Much like a lab notebook where a wet-lab experimentalist might have both the experimental protocol and notes on the specific experiment, a Jupyter notebook allows you to have code and notes in the same notebook.

Visit https://colab.research.google.com/ and click on Examples or, if you’re already in colab, File -> Open notebook. Then in the resulting window, click on Examples.

Google offers many example notebooks:

When you first open a colab notebook, it may not be ready to execute code. Click on Connect (circled in figure) to connect to a hosted runtime. When you see a green checkmark, you’re all set to run code in your notebook.

Google offers a basic colab experience for free. Hosted runtime machines consume computing resources which will be shut down if you’re not active in the notebook. If you see an “Are you still there?” window during this workshop, complete the prompt so your colab notebooks stays active.

If you see Connect or Reconnect, you’ve been disconnected from a hosted runtime and you’ll need to reconnect. Any work you did in the notebook is likely to be stale and you’ll need to Runtime -> Run all (Ctrl+F9).

Note on keyboard shortcuts for Mac

In colab, Macs can use Ctrl+F9 OR ⌘+F9. In other Jupyter notebook environments, Ctrl+F9 may not be an option for Mac. For the rest of this workshop, we’ll use indicate Ctrl+<keystroke> for simplicity. Mac users should keep in mind that using Command (⌘) in lieu of Ctrl is an option.

Disabling the Generative AI feature

Notice in the code cell, the word generate is a hyperlink to colab’s new generative AI feature. Because this is a little distracting when you accidentally click on the link, we recommend you disable this feature during the workshop.

Click on the settings ⚙️ icon in the upper right hand corner of your colab notebook. Select AI Assistance and check “Hide generative AI features”.

Variables

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Any Python interpreter can be used as a calculator:

PYTHON

3 + 5 * 4

OUTPUT

23

Run code cell and insert new cell (Alt/Option + Enter)

In Jupyter notebook, there are many ways to run a code cell and insert a new cell.
To do this with one keyboard shortcut, Alt/Option + Enter.

Alternatively, you can Ctrl + Enter to run the currently selected cell. Then use the Escape key to enter Command mode, then press B to insert a new cell below the current cell (or A to insert above the current cell).

Using the graphical interface in colab, you can click the ▶️ symbol at the left hand side of the cell. Then click the +Code button.

Doing arithmetic using Python is ok but not very interesting. To do anything useful with data, we need to assign its value to a variable. In Python, we can assign a value to a variable, using the equals sign =. For example, we can track the weight of a patient who weighs 60 kilograms by assigning the value 60 to a variable weight_kg:

PYTHON

weight_kg = 60

From now on, whenever we use weight_kg, Python will substitute the value we assigned to it. In layperson’s terms, a variable is a name for a value.

In Python, variable names:

• can include letters, digits, and underscores
• cannot start with a digit
• are case sensitive.

This means that, for example:

• weight0 is a valid variable name, whereas 0weight is not
• weight and Weight are different variables

Types of data

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Python knows various types of data. Three common ones are:

• integer numbers
• floating point numbers, and
• strings.

In the example above, variable weight_kg has an integer value of 60. If we want to more precisely track the weight of our patient, we can use a floating point value by executing:

PYTHON

weight_kg = 60.3

To create a string, we add single or double quotes around some text. To identify and track a patient throughout our study, we can assign each person a unique identifier by storing it in a string:

PYTHON

patient_id = '001'

Using Variables in Python

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Once we have data stored with variable names, we can make use of it in calculations. We may want to store our patient’s weight in pounds as well as kilograms:

PYTHON

weight_lb = 2.2 * weight_kg

We might decide to add a prefix to our patient identifier:

PYTHON

patient_id = 'inflam_' + patient_id

Built-in Python functions

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To carry out common tasks with data and variables in Python, the language provides us with several built-in functions. To display information to the screen, we use the print function:

PYTHON

print(weight_lb)
print(patient_id)

OUTPUT

132.66
inflam_001

When we want to make use of a function, referred to as calling the function, we follow its name by parentheses. The parentheses are important: if you leave them off, the function doesn’t actually run! Sometimes you will include values or variables inside the parentheses for the function to use. In the case of print, we use the parentheses to tell the function what value we want to display. We will learn more about how functions work and how to create our own in later episodes.

We can display multiple things at once using only one print call:

PYTHON

print(patient_id, 'weight in kilograms:', weight_kg)

OUTPUT

inflam_001 weight in kilograms: 60.3

We can also call a function inside of another function call. For example, Python has a built-in function called type that tells you a value’s data type:

PYTHON

print(type(60.3))
print(type(patient_id))

OUTPUT

<class 'float'>
<class 'str'>

Moreover, we can do arithmetic with variables right inside the print function:

PYTHON

print('weight in pounds:', 2.2 * weight_kg)

OUTPUT

weight in pounds: 132.66

The above command, however, did not change the value of weight_kg:

PYTHON

print(weight_kg)

OUTPUT

60.3

To change the value of the weight_kg variable, we have to assign weight_kg a new value using the equals = sign:

PYTHON

weight_kg = 65.0
print('weight in kilograms is now:', weight_kg)

OUTPUT

weight in kilograms is now: 65.0

Variables as Sticky Notes

A variable in Python is analogous to a sticky note with a name written on it: assigning a value to a variable is like putting that sticky note on a particular value.

Using this analogy, we can investigate how assigning a value to one variable does not change values of other, seemingly related, variables. For example, let’s store the subject’s weight in pounds in its own variable:

PYTHON

# There are 2.2 pounds per kilogram
weight_lb = 2.2 * weight_kg
print('weight in kilograms:', weight_kg, 'and in pounds:', weight_lb)

OUTPUT

weight in kilograms: 65.0 and in pounds: 143.0

Everything in a line of code following the ‘#’ symbol is a comment that is ignored by Python. Comments allow programmers to leave explanatory notes for other programmers or their future selves.

Similar to above, the expression 2.2 * weight_kg is evaluated to 143.0, and then this value is assigned to the variable weight_lb (i.e. the sticky note weight_lb is placed on 143.0). At this point, each variable is “stuck” to completely distinct and unrelated values.

Let’s now change weight_kg:

PYTHON

weight_kg = 100.0
print('weight in kilograms is now:', weight_kg, 'and weight in pounds is still:', weight_lb)

OUTPUT

weight in kilograms is now: 100.0 and weight in pounds is still: 143.0

Since weight_lb doesn’t “remember” where its value comes from, it is not updated when we change weight_kg.

Check Your Understanding

What values do the variables mass and age have after each of the following statements? Test your answer by executing the lines.

PYTHON

mass = 47.5
age = 122
mass = mass * 2.0
age = age - 20

Show me the solution

OUTPUT

`mass` holds a value of 47.5, `age` does not exist
`mass` still holds a value of 47.5, `age` holds a value of 122
`mass` now has a value of 95.0, `age`'s value is still 122
`mass` still has a value of 95.0, `age` now holds 102

Sorting Out References

Python allows you to assign multiple values to multiple variables in one line by separating the variables and values with commas. What does the following program print out?

PYTHON

first, second = 'Grace', 'Hopper'
third, fourth = second, first
print(third, fourth)

Show me the solution

OUTPUT

Hopper Grace

Seeing Data Types

What are the data types of the following variables?

PYTHON

planet = 'Earth'
apples = 5
distance = 10.5

Show me the solution

PYTHON

print(type(planet))
print(type(apples))
print(type(distance))

OUTPUT

<class 'str'>
<class 'int'>
<class 'float'>

Key Points

• Basic data types in Python include integers, strings, and floating-point numbers.
• Use variable = value to assign a value to a variable in order to record it in memory.
• Variables are created on demand whenever a value is assigned to them.
• Use print(something) to display the value of something.
• Use # some kind of explanation to add comments to programs.
• Built-in functions are always available to use.