Python Language Overview

BCH 519
Spring 2021

Andrew E. Bruno
aebruno2@buffalo.edu

Course Goals

Learn python to formulate solutions to bioinformatics problems

Book

Python for Biologists by Dr. Martin Jones
https://pythonforbiologists.com/introduction/

What is Python?

High-level, general purpose, dynamic programming language
Created by Guido van Rossum in 1989
Why is it called python?

"When he began implementing Python, Guido van Rossum was also reading the published scripts from "Monty Python's Flying Circus", a BBC comedy series from the 1970s. Van Rossum thought he needed a name that was short, unique, and slightly mysterious, so he decided to call the language Python."

– General Python FAQ

Programming in Python

Running Python programs

Run python program from the Linux command line:

$ python3 myprog.py

Python versions

Python 2 vs Python 3
Python 2.x is legacy use 3
Default python version on vortex is 2.7.5
To use python 3 just run python3:

$ python -V
Python 2.7.5

$ python3 -V
Python 3.6.8

$ module load bioconda/py37-biopython
$ python -V
Python 3.7.6

Python Documentation

Code to all exercises

In course project directory on vortex

/projects/academic/courses/bch519/spring21/exercises

Basic Syntax Overview

Exercise 1: First Python Program

Type the following code into a text file named ex1.py

print("Hello World")
print("Just what do you think you're doing, Dave?")
print('Seq1: "hg19" ATCGCTGCAT')

Then run in the terminal by typing:

$ python3 ex1.py
Hello World
Just what do you think you're doing, Dave?
Seq1: "hg19" ATCGCTGCAT

What do errors look like?

Edit ex1.py and remove the first ‘p’ in print on the first line

rint("Hello World")

Then re-run in the terminal by typing:

$ python3 ex1.py
  File "ex1.py", line 1
    rint "Hello World"
                     ^
SyntaxError: invalid syntax

Exercise 1: What we learned

Python programs are text files
File names (typically) end in .py
print displays the given text (without quotations)
The text inside quotes is called a string
Python reports errors if the syntax is not correct

Exercise 2: Comments

Type the following code into a text file named ex2.py

# This is a comment, here to explain what the code is doing
# Anything after the # is ignored by python

print("Hello # World")  # comments can be here

#
# HAL: It can only be attributable to human error.
#
print("Just what do you think you're doing, Dave?")

Then run in the terminal by typing:

$ python3 ex2.py
Hello # World
Just what do you think you're doing, Dave?

Exercise 2: What we learned

# Comments are important. They help yourself and others understand your code
# Anything after the # is ignored by python
# Good practice to always comment your code!

Exercise 3: Numbers

Type the following code into a text file named ex3.py

print(0 + 1 + 1 + 2 + 3 + 5 + 8)
print(22 % 5)
print(3 * 4 + 6 / 3)

Then run in the terminal by typing:

$ python3 ex3.py
20
2
14

Exercise 3: What we learned

Python can do basic math
Order of operations: (3 * 4) + (6 / 3)
% = modulo operator

Exercise 4: Variables

Type the following code into a text file named ex4.py

seq_count = 10
gene = "NM_130786"
total = seq_count * 50
avg = total / seq_count
print(f"Gene {gene} has {seq_count} sequences")
print(f"The average number of sequences is: {avg}")
print(f"There's a total of {total} sequences")

Then run in the terminal by typing:

$ python3 ex4.py
On gene NM_130786 there are 10 sequences
The average number of sequences is: 50.0
There's a total of 500 sequences

Exercise 4: What we learned

Variable is a named reference to a value
Variables can be printed in human-readable form using f-strings
Values are converted to strings. {} are placholders of variables
https://docs.python.org/3/tutorial/inputoutput.html

Exercise 5: Strings

Type the following code into a text file named ex5.py

first = 'Marty'
last = "McFly"
gigawatts = 1.21

full_name = first + ' ' + last
greeting = f"Hello {first} {last}"

print(full_name)
print(greeting)
print(f'Achtung {first}, {gigawatts} gigawatts!')
print(f'{gigawatts:.3f} gigawatts')
# Another way to format strings
print("First: {0} Last: {1}".format(first, last))

Exercise 5: Output

Then run in the terminal by typing:

$ python ex5.py
Marty McFly
Hello Marty McFly
Achtung Marty, 1.21 gigawatts!
1.210 gigawatts
First: Marty Last: McFly

Exercise 5: What we learned

Double quotes or single quotes may be used around literal strings
the + operator concatenates strings together
f-strings can be used to concatenate strings
{myvar:.3f} an optional ‘:’ and format specifier can follow the variable. This formats to 3 decimal places

Exercise 6: Printing Strings

Type the following code into a text file named ex6.py

chrom = 'chrom1'
start = 1002
end = 1012
print("chrom\tstart\tend")
print(f"{chrom}\t{start}\t{end}")
print("{0}:{1}-{2}, start = {1}".format(chrom, start, end))

print('What\'s the Gene\'s \\ fasta')
fasta = """>NM_130786
GGGCCTCATT
GCTGCAGACG
"""
print(fasta)

substr = chrom[1:4]  # extract substring
print(substr)

Exercise 6: Output

Then run in the terminal by typing:

$ python3 ex6.py
chrom   start   end
chr1    1002    1012
chr1:1002-1012, start = 1002
What's the Gene's \ fasta
>NM_130786
GGGCCTCATT
GCTGCAGACG

hro

Exercise 6: What we learned

Use a backslash \ to escape special characters
\t prints a TAB character \n prints a newline
''' triple-quote defines strings with many lines of text
'{0} {1} {2} {1}' can re-use placeholders in format string
chrom[1:4] extracts a substring, starting from index 1 up to index 4 (not including)

index:  0 1 2 3 4 5
string: c h r o m 1 
          * * *

sub-string: hro

Control Structures

Conditionals

A control structure controls the flow of a program
- if = choice of whether to execute a block of code
- if-elif-else = multiple block choices
- for loops = repeat a block multiple times
- while loops = repeat a block multiple times
Uses boolean expressions as conditions

Basic structure of the `if` statement

if boolean_condition:
    code_block 
elif: other_condition:
    code_block
else:
    code_block

Exercise 7: Conditionals

Type the following code into a text file named ex5.py

if 5 > 4:
    print("Five is greater than four")

if "Hello" == "HELLO":
    print("This will not print")

grade = 83.5;
if grade < 50:
    print("D")
elif grade < 75:
    print("C")
elif grade < 90:
    print("B")
else:
    print("A")

Exercise 7: Output

Then run in the terminal by typing:

$ python3 ex7.py
Five is greater than four
B

Example flow control

Boolean Logic

p	q	p and q	p or q
T	T	T	T
T	F	F	T
F	T	F	T
F	F	F	F

Exercise 8: Boolean Operators

Join two or more boolean expressions with and/or logic

a = 10
b = 5
c = 7

print(a > b and a > c)  # TRUE
print(c > a and c > b)  # FALSE
print(a > b and b > c)  # FALSE
print(c > a or c > b)   # TRUE 
print(a < c or b > c)   # FALSE

Exercise 7 & 8: What we learned

Conditional constructs allow execution of code given some condition is true/false
Join two or more boolean expressions with and/or logic operators
Spacing is important!
Code under the if needs to be indented 4 spaces

Python builtin operators

Arithmetic/Boolean		Comparison operators
+	addition	==	equality
-	subtraction	!=	inequality
*	multiplication	<	strictly less than
/	division	>	strictly greater than
**	exponentiation	<=	less than or equal
%	modulo	>=	greater than or equal
and	and	is	object identity
or	or	is not	negated object identity
not	not

Loops

Allows execution of the same code a number of times

Basic structure of looping constructs

while boolean_condition:
    code_block

for i in range(0,10):
    code_block

for i in ['X','Y','Z']:
    code_block

Example flow control

Exercise 9: Loops

Type the following code into a text file named ex9.py

x = 0
while x != 5:
    print(x)
    x = x + 1

message = "Hello"
for char in message:
    print(char)

chroms = ['chr1', 'chr2', 'chr3']
for c in chroms:
    if c == 'chr2':
        continue

    print(c)

Exercise 9: Output

Then run in the terminal by typing:

$ python3 ex9.py
0
1
2
3
4
H
e
l
l
o
chr1
chr3

Exercise 10: Nesting loops

Loops can also be nested
For example, looping through rows/cols of a matrix

for i in range(0, 5):
    for j in range(0, 5):
        print("row: {} col: {}".format(i,j))

Exercise 9 & 10: What we learned

loop constructs allow execution of code multiple times
code under the for needs to be indented 4 spaces
for loops over a list of values (iterable)
continue command starts next iteration of the loop - Loops can be nested
strings are iterable

Executing Python programs

To run a Python program from the Linux command line:

$ python3 myprogram.py

Alternatively, ensure the first line of your script contains:

#!/usr/bin/env python3

Make your script executable and run:

$ chmod +x myprogram.py
$ ./myprogram.py

Python Language Overview

BCH 519Spring 2021

Course Goals

Learn python to formulate solutions to bioinformatics problems

Book

What is Python?

Programming in Python

Running Python programs

Python versions

Python Documentation

Code to all exercises

Basic Syntax Overview

Exercise 1: First Python Program

Type the following code into a text file named ex1.py

Then run in the terminal by typing:

What do errors look like?

Edit ex1.py and remove the first ‘p’ in print on the first line

Then re-run in the terminal by typing:

Exercise 1: What we learned

Exercise 2: Comments

Type the following code into a text file named ex2.py

Then run in the terminal by typing:

Exercise 2: What we learned

Exercise 3: Numbers

Type the following code into a text file named ex3.py

Then run in the terminal by typing:

Exercise 3: What we learned

Exercise 4: Variables

Type the following code into a text file named ex4.py

Then run in the terminal by typing:

Exercise 4: What we learned

Exercise 5: Strings

Type the following code into a text file named ex5.py

Exercise 5: Output

Then run in the terminal by typing:

Exercise 5: What we learned

Exercise 6: Printing Strings

Type the following code into a text file named ex6.py

Exercise 6: Output

Then run in the terminal by typing:

Exercise 6: What we learned

Control Structures

Conditionals

Basic structure of the if statement

Exercise 7: Conditionals

Type the following code into a text file named ex5.py

Exercise 7: Output

Then run in the terminal by typing:

Example flow control

Boolean Logic

Exercise 8: Boolean Operators

Join two or more boolean expressions with and/or logic

Exercise 7 & 8: What we learned

Python builtin operators

Loops

Allows execution of the same code a number of times

Basic structure of looping constructs

Example flow control

Exercise 9: Loops

Type the following code into a text file named ex9.py

Exercise 9: Output

Then run in the terminal by typing:

Exercise 10: Nesting loops

Exercise 9 & 10: What we learned

Executing Python programs

To run a Python program from the Linux command line:

Alternatively, ensure the first line of your script contains:

Make your script executable and run:

Homework #2

Due: 2021-02-23 09:00:00

BCH 519
Spring 2021

Basic structure of the `if` statement