Best viewed in a Jupyter Notebook

This tutorial is best viewed in a Jupyter notebook! You can load this notebook one of the following ways

Run on the GTN with JupyterLite (in-browser computations)

1. Click to Launch JupyterLite

Launching the notebook in Jupyter in Galaxy

1. Instructions to Launch JupyterLab
2. Open a Terminal in JupyterLab with File -> New -> Terminal
3. Run wget https://training.galaxyproject.org/training-material/topics/data-science/tutorials/python-flow/data-science-python-flow.ipynb
4. Select the notebook that appears in the list of files on the left.

Downloading the notebook

1. Right click one of these links: Jupyter Notebook (With Solutions), Jupyter Notebook (Without Solutions)
2. Save Link As..

“Flow Control” is how we describe when we change the flow of code’s execution, based on some conditions. Here we’ll learn how to take different actions depending on what data out program sees, or how to run code only if some condition is true.

Comment

This tutorial is significantly based on the Carpentries Programming with Python and Plotting and Programming in Python, which are licensed CC-BY 4.0.

Adaptations have been made to make this work better in a GTN/Galaxy environment.

Agenda

In this tutorial, we will cover:

1. Comparators
2. Conditionals
3. Multiple Branches
4. Combining Tests
5. Inverting Conditions
6. Ranges
7. Exercises

Comparators

In Python we have the following comparators to do compare two values

• >: greater than
• <: less than
• ==: equal to
• !=: does not equal
• >=: greater than or equal to
• <=: less than or equal to

They’re all “binary” comparators, we can only compare two values at a time.

print(37 < 38)
print(38 < 38)
print(39 < 38)

These print out True or False, these are the two possible values of the boolean datatype in Python.

We can use <= to check if it’s less than or equal to:

print(19 <= 20)
print(20 <= 20)
print(21 <= 20)

And we can use == for comparing numbers in Python

print(11 == 11)
print(11 != 11)
print(22 != 33)

And now that we can compare numbers, we can start doing useful things with them!

Conditionals

We can ask Python to take different actions, depending on a condition, with an if statement:

num = 37
if num > 100:
    print('greater')
else:
    print('not greater')
print('done')

The second line of this code uses the keyword if to tell Python that we want to make a choice. If the test that follows the if statement is true, the body of the if (i.e., the set of lines indented underneath it) is executed, and “greater” is printed. If the test is false, the body of the else is executed instead, and “not greater” is printed. Only one or the other is ever executed before continuing on with program execution to print “done”:

Conditional statements don’t have to include an else. If there isn’t one, Python simply does nothing if the test is false:

num = 53
print('before conditional...')
if num > 100:
    print(f'{num} is greater than 100')
print('...after conditional')

Question: If behaviour

Try changing the num value and see what happens for different values.

What happens if num is a:

1. 202
2. 3.145
3. “test”
4. 100.000001

Solution

1. Condition is activated!
2. Nothing, but not because it is a float! Because it’s less than 100
3. Traceback, a TypeError, you cannot compare strings with integers
4. Condition is activated!

Multiple Branches

But what if you want more branches? What if you need to handle more cases? elif to the rescue!

We can chain several tests together using elif, which is short for “else if”.

if todays_temperature > 30:
    print("Wear shorts! Remember your sunscreen")
elif todays_temperature > 20:
    print("It's nice weather finally! Gasp!")
elif todays_temperature < 10:
    print("Time to bundle up!")
else:
    print("Dress normally")

Tip: If/Elif/Elif/Elif/Else:

if/elif/else cases follow these rules:

• must start with an if
• can have 0 or more elif conditions
• can have 0 or 1 else condition (if no else condition is supplied, it’s equivalent to else: <nothing>)

Each of these three sections is a branch, the code pauses, and chooses to go down one of the branches based on the conditions.

The following Python code uses elif to print the sign of a number.

num = -3

if num > 0:
    print(f'{num} is positive')
elif num == 0:
    print(f'{num} is zero')
else:
    print(f'{num} is negative')

NB: To test for equality we use a double equals sign == rather than a single equals sign = which is used to assign values.

Combining Tests

We can also combine tests using and and or. and is only true if both parts are true:

a = 1
b = -1
if (a > 0) and (b <= 0):
    print('both parts are true')
else:
    print('at least one part is false')

Question: Predict what happens

Predict the outcomes of the following values of a and b above. Predicting what you think the code will do is a useful skill to practice

1. a = 0; b = -1
2. a = 0; b = 10
3. a = 4; b = -22
4. a = 99; b = 99

Solution

1. at least one part is false
2. at least one part is false
3. both parts are true
4. at least one part is false

while or is true if at least one part is true:

a = 1
b = -1
if (a < 0) or (b > 0):
    print('at least one test is true')

Tip: `True` and `False`

True and False are special words in Python called booleans, which represent truth values. A statement such as 1 < 0 returns the value False, while -1 < 0 returns the value True.

True and False booleans are not the only values in Python that are true and false. In fact, any value can be used in an if or elif. This is commonly used to check, for instance, if a string is empty or if some data is provided:

if '':
    print('empty string is true')
if 'word':
    print('word is true')

You can also use it to check if a list is empty or full:

if []:
    print('empty list is true')
if [1, 2, 3]:
    print('non-empty list is true')
# The last statement is equivalent to:
if len([1, 2, 3]) > 0:
    print('non-empty list is true')

Or you can check if a number is zero, or non-zero:

if 0:
    print('zero is true')
if 1:
    print('one is true')

Inverting Conditions

Sometimes it is useful to check whether some condition is not true. The Boolean operator not can do this explicitly. After reading and running the code below, write some if statements that use not to test the rule that you formulated in the previous question. not is a unary (not binary) operator: it only takes a single value

if not '':
    print('empty string is not true')
if not 'word':
    print('word is not true')
if not not True:
    print('not not True is true')

Ranges

Python makes it super easy to check if a number is within a range.

quality_score = 32 # Try out different values!

if quality_score > 40:
    print("Your data is a bit sus")
elif 20 < quality_score <= 40:
    print("Hey that looks ok")
elif 4 < quality_score <= 20:
    print("Oh you did nanopore sequencing")
else:
    print("It shouldn't be *that* bad. Try again.")

There are two important points here:

• 20 < x < 40 is equivalent to 20 < x and x < 40, checking both sides of the condition, to make sure it’s greater than one value and smaller than another
• Note that we checked in the second case 20 < x and then in the third we had to check x <= 20. If we had not had a <= on one side, what would have happened to 20? It would have gone straight to else!

Exercises

Question

ifs, elifs and elses get evaluated in blocks. Look at the following code and list the lines that are part of a single block.

1.  if x:
2.      # ..
3.  if y:
4.      # ..
5.  elif z:
6.      # ..
7.  if q:
8.      # ..
9.  else:
10.     # ..
11. elif t:
12.     # ..
13. else e:
14.     # ..

Solution

“Blocks” of if/elif/elses

• must start with an if
• can have 0 or more elif conditions
• can have 0 or 1 else condition (if no else condition is supplied, it’s equivalent to else: <nothing>)

The above blocks are parsed together, you could not insert a print anywhere within the blocks, but between the blocks it would work.

• 1-2, Just an if by itself. There’s no elif, or else, so that’s the end of that block
• 3-6, if and elif get evaluated, there is no else, so that’s the end of that block
• 7-10, if and else is fine
• 11-14, error! This is missing an if case, it will fail with a syntaxerror.

# Test code here.

Question: How Many Paths?

Consider this code:

if 4 > 5:
    print('A')
elif 4 == 5:
    print('B')
elif 4 < 5:
    print('C')

Which of the following would be printed if you were to run this code? Why did you pick this answer?

1. A
2. B
3. C
4. B and C

Solution

C gets printed because the first two conditions, 4 > 5 and 4 == 5, are not true, but 4 < 5 is true.

# Test code here.

Question: Close Enough

Write some conditions that print True if the variable a is within 10 of the variable b and False otherwise. Compare your implementation with your partner’s: do you get the same answer for all possible pairs of numbers?

Tip: abs

There is a [built-in function abs][abs-function] that returns the absolute value of a number:

print(abs(-12))

12

Solution: 1

a = 5
b = 5.1

if abs(a - b) <= 10:
    print('True')
else:
    print('False')

Solution: 2

print(abs(a - b) <= 10)

This works because the Booleans True and False have string representations which can be printed.

# Test code here.

Question: Pitfalls

A integer number between 0 and 100 will be provided to this function. Answer these two questions:

• Will it always print something? If not, which value(s) fail?
• Can you find any numbers the programmer explicitly wanted to handle, that aren’t handled as expected?

num = 42 # Randomly chosen so the code will execute, try changing it around.
if num > 90:
    print("great score")
elif num < 32:
    print("Very cold")
elif num >= 86:
    print("Almost")
elif num == 86:
    print("It's exactly this value!")
elif 32 < num < 58:
    print("Getting warmer")
elif 57 < num <= 86:
    print("Everything else goes here")

Solution

1. No, it won’t. 32 is the only value there that doesn’t print anything. You can either do x < 57 and later 57 <= x to test the bigger and smaller values, or you can make use x < 57 and 56 < x, which have the same results, but only with integers. If your code accepted a float, e.g. 56.5, both of those tests would be true. So x < 57 and later 57 <= x is the preferred way to write that.
2. 86 is the most obvious solution to this, the programmer added a check specifically to see if the value was 86, but instead it’s caught by the previous case.

num = 42 # Randomly chosen so the code will execute, try changing it around.
if num > 90:
    print("great score")
elif num < 32:
    print("Very cold")
elif num >= 86:
    print("Almost")
elif num == 86:
    print("It's exactly this value!")
elif 32 < num < 58:
    print("Getting warmer")
elif 57 < num <= 86:
    print("Everything else goes here")

Tip: Why a synthetic example like this?

Complicated if/elif/else cases are common in code, you need to be able to spot these sort of issues. For example there are large if/else cases in the Galaxy codebase, sometimes nested even, and being ale to predict their behaviour is really important to being able to work with the code. Missing else cases are sometimes important, sometimes a bug, sometimes just the code hasn’t been implemented yet, which is why we always write good code comments!

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Use if condition to start a conditional statement, elif condition to provide additional tests, and else to provide a default.

• The bodies of the branches of conditional statements must be indented.

• Use == to test for equality.

• X and Y is only true if both X and Y are true.

• X or Y is true if either X or Y, or both, are true.

• Zero, the empty string, and the empty list are considered false; all other numbers, strings, and lists are considered true.

• True and False represent truth values.

• not can be used to invert the condition

Frequently Asked Questions

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.

Citing this Tutorial

1. carpentries, Helena Rasche, Donny Vrins, Bazante Sanders, Python - Flow Control (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/data-science/tutorials/python-flow/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{data-science-python-flow,
author = "carpentries and Helena Rasche and Donny Vrins and Bazante Sanders",
	title = "Python - Flow Control (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/data-science/tutorials/python-flow/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Go Further

Do you want to extend your knowledge? Follow one of our recommended follow-up trainings:

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-flow/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

Feedback

No feedback has been recieved yet for this training. Be the first one by filling in the feedback form from above.