Programming with Python

Duke UPGG Informatics Orientation Bootcamp

Audience: Many Different Backgrounds

1. New to programming, never seen any code before
2. Have done some programming, but not confident with the subject
3. Extensive programming, confident with the subject
4. Former software engineer, professional

Today's Lesson: Fundamentals of Programming

• Start with the fundamentals so everyone is on the same page
• Build a foundation for lessons later in the workshop

How does one start to learn programming?

Practice Practice Practice!

• Just like learning how to ride a bike, you start by doing
• No wrong choice on what programming language to start with or learn
  • What is important are the fundamental concepts for writing code, not the specifics of the language
  • Lots of concepts are important in any programming language you want to use

Why Python?

• It is a general purpose programming language popular among many disciplines
  • Ex/ scientific computing, software engineering, finance
• Large community among scientists
• It’s free, well-documented, and runs everywhere
• Relatively quick to start using, but there is a lot to learn!

Percent of pull requests on GitHub by language in Q1 of 2022.

Data from: https://madnight.github.io/githut/#/pull_requests/2022/1

Percent of searches for tutorials on Google

Data from: https://pypl.github.io/PYPL.html

Goals: Write and Run Programs

• Cover common data types and functions
• Making decisions in a program with if statements
• Writing for loops to apply code to a group of data
• Writing our own functions
• Work with files and libraries
• Know where to look for more help

Expectations

• This is alot of material
  • Especially for someone new to programming
• I will do my best to go through the material at an appropriate pace
• Feel free to let me know if I am:
  • Going too fast
  • Need to explain something in more detail
  • Provide more examples
  • etc.

Expectations

• If you are having technical issues, use a sticky note
  • This will be taught with live coding, I will probably have technical issues
• Feel free to ask me questions
• You can also use a sticky note to signal a helper or another instructor to help you with a question
• Or ask a neighbor

Download

- Download the python-fasta.zip file from the course website - Syllabus.

- Unzip it and place on your Desktop:

python-fasta/
  ae.fa
  ls_orchid.fasta

1. Open Anaconda Navigator (installed with Anaconda)

2. Click to launch Jupyter Notebook

Begin Jupyter Notebook

Recap and Exercise: Data Types and Variables

Data Types

Numeric:

- Integer: 1, 76, 400

- Float: -1.2, 0.5, 3.1415926 (Use a decimal point)

- Boolean: True, False

Text:

- Strings: ‘ACTGACAG' (Wrap in quotes)

Strings

Strings can be created with quotes or double quotes:

name = 'Daniel'

Access individual letters as strings with [] (starting at 0)

name[0] # D
name[1] # a

Check if a letter exists in a string

'a' in name # True
'a' not in name # False

Variables

Assign variables with equals

x = 2

Access variables by name

print(x) # 2

Variables work like sticky notes, they’re just a label

What do we know?

Our sequence is a string, in seq

Strings are sequences of characters, each at a numbered position (starting from 0)

We can extract characters as strings with square brackets [ ]

We can combine strings together with +

Exercise: Reverse

Write some code that reverses the sequence in seq.

It should:

1. Create an empty string variable rev

rev = ''

2. Loop over the items in seq, adding these to rev in reversed order

3. Print the contents of rev

Recap: Loops, Dictionaries, Lists, and Conditionals

Loops

Write a loop with for item in collection:


for letter in word:
  print(letter)

Always put a colon at the end of the line, indented lines are run for every item in the collection

Complementing

• We can loop over all the bases in a sequence
• Each base has a complement that we should substitute
• We can use a Dictionary to store this mappping.

Dictionaries and Lists

Create dictionaries with {}, lists with []

nucs = {'A': 5, 'C': 4, 'T': 8}
counts = [5,4,8]

Both accessed with [] - dictionaries by key, lists by index

nucs['A'] # 5
counts[0] # 5

nucs['A'] = 3 # now 3
counts[0] = 3 # now 3

GC-content percentage

• Calculated as (G + C) / (A + T + G + C)
• Create a GC count variable and an ATGC count variable
  • Loop over each base in the sequence
    • If G, add 1 to GC count
    • If C add 1 to GC count
    • For everything, add 1 to ATGC count

Conditionals

# Test c1 for True or False
if c1:
    print("c1 was True")
# c1 was False, check c2
elif c2:
    print("c1 False but c2 True")
# All checks False
else:
    print("Both False")

Exercise: Using Functions

bases = 'adenine cytosine guanine thymine' Write some code that:

• Makes a list of these bases from the string
• Uppercases the names (e.g. ['ADENINE', ...])
• Reverses the order (e.g. ['THYMINE',...])

Hint: Use help(str) and help(list) to see what functions are available for strings and lists

Bonus: Write a for loop to print the first letter of each (e.g. A, C, ...)

Exercise: Update the Reverse Function

Strings can be reversed with this special slicing notation: [::-1]


s = 'abc'
r = s[::-1]
print(r)

cba

Update reverse() function to use [::-1] instead of a loop.

Do we need to do anything to complement()? 
 What about reverse_complement()?

Recap and Exercise: Making Functions and Reading Files

Functions

Calling functions: length = len('abc')

• Defining functions:

  def double(x):
    return x * 2

• Composing functions:

  def reverse_complement(seq):
    return reverse(complement(seq))

Avoid using global variables in functions

Reading files

• Open a file with the open() function:

  f = open('ae.fa')

• Loop over lines, and strip() each one

  for line in f:
    print(line.strip())

• Close with f.close()

Exercise: Reading a Fasta File

• Write a function, read_fasta(filename) that:
  • Takes 1 argument: filename
  • Reads the file line-by-line
  • Strips/combines the lines into one long line
  • Skips the line if it contains a '>' character

Scripts

• Put code in a file, give it the .py extension
• Read command line-arguments from sys.argv:

import sys
print(sys.argv[0])
print(sys.argv[1])

$ python script.py hello
script.py
hello

• Check the length of sys.argv to be helpful!

Summary

• We introduced several data types inculding:
  • Integers, Floats, Strings, Dictionaries, Lists
• How to assign values to variables and use them
• Making choices using conditional statements
• Writing for loops to perform a task over a group of data
• Making our own functions
• Work with files and libraries
• Help function: help()

Questions?