Practical issues¶
- Course website: https://uppsala.instructure.com/courses/99844
- Course lectures streamed from Uppsala and Umeå
- TAs on each site
- Short lectures with many breaks
- Schedule times are approximate
Schedule¶
To start with¶
- Has everyone managed to log in to Canvas?
- Has everyone managed to install Python?
- Have you managed to run the test script?
- Have you installed notebooks? (optional)
- Canvas tour
- PyQuizzes
What is programming?¶
Wikipedia:
"Computer programming is the process of building and designing an executable computer program for accomplishing a specific computing task"
What can we use it for?¶
Endless possibilities!
- reverse complement DNA
- custom filtering of VCF files
- plotting of results
- all excel stuff!
Python versions¶
| Old versions | Python 3 |
|---|---|
| Python 1.0 - January 1994 | Python 3.0 - December 3, 2008 |
| Python 1.0 - January 1994 | Python 3.1 - June 27, 2009 |
| Python 1.2 - April 10, 1995 | Python 3.2 - February 20, 2011 |
| Python 1.3 - October 12, 1995 | Python 3.3 - September 29, 2012 |
| Python 1.4 - October 25, 1996 | Python 3.4 - March 16, 2014 |
| Python 1.5 - December 31, 1997 | Python 3.5 - September 13, 2015 |
| Python 1.6 - September 5, 2000 | Python 3.6 - December 23, 2016 |
| Python 2.0 - October 16, 2000 | Python 3.7 - June 27, 2018 |
| Python 2.1 - April 17, 2001 | Python 3.8 - October 14, 2019 |
| Python 2.2 - December 21, 2001 | Python 3.9 - October 5, 2020 |
| Python 2.3 - July 29, 2003 | Python 3.10 - October 4, 2021 |
| Python 2.4 - November 30, 2004 | Python 3.11 - October 24 2022 |
| Python 2.5 - September 19, 2006 | Python 3.12 - October 2 2023 |
| Python 2.6 - October 1, 2008 | Python 3.13 - October 2024 |
| Python 2.7 - July 3, 2010 |
Course content
- Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments
- Different ways to control program flow using loops and conditional tests
- Regular expressions and pattern matching
- Writing functions and best-practice ways of making them usable
- Reading from and writing to files
- Code packaging and Python libraries
- How to work with biological data using external libraries.
Learning outcomes
At the end of the course, you should be able to:
- Use variables and exlain how operators work
- Process data using loops
- Separate data using if/else statements
- Use functions to read and write to files
- Describe their own approach to a coding task
- Understand the difference between functions and methods
- Be able to read the documentation for built-in functions/methods
- Give examples of use cases for dictionaries
- Write data to a simple dictionary
- Understand the concept and syntax of a function
Learning outcomes, cont.
At the end of the course, you should be able to:
- Write basic functions for processing data
- Describe pandas dataframes
- Give examples of how to use pandas for processing data
- Explain how regex can be used
- Define the python syntax for regex
- Combine basic concepts to create functional stand-alone programs to process data
- Write file processing Python programs that produce output to the terminal and/or external files
- Explain how to debug and further develop your skills in Python after the course
Some good advice¶
- 5 days to learn Python is not much
- Amount of information will decrease over days
- Complexity of tasks will increase over days
- Read the error messages!
- Save all your code
How to seek help:
- Ask your neighbour
- Ask an assistant
You will look like this:¶
Day 1¶
- Types and variables
- Operations
- Loops
- if/else statements
Example of a simple Python script¶
In [29]:
# A simple loop that adds 2 to a number
i = 0
while i < 10:
u = i + 2
print('u is' + str(u))
i += 1
u is2 u is3 u is4 u is5 u is6 u is7 u is8 u is9 u is10 u is11
Literals define values¶
In [30]:
'this is a string'
"this is also a string"
3 # here we can put a comment so we know that this is an integer
3.14 # this is a float
True # this is a boolean
type(True)
Out[30]:
bool
Collections¶
In [31]:
[3, 5, 7, 4, 99] # this is a list of integers
('a', 'b', 'c', 'd') # this is a tuple of strings
{'a', 'b', 'c'} # this is a set of strings
{'a':3, 'b':5, 'c':7} # this is a dictionary with strings as keys and integers as values
type([3, 5, 7, 4, 99])
Out[31]:
list
What operations can we do with different values?¶
That depends on their type:
In [32]:
'a string'+' another string'
2 + 3.4
'a string ' * 3
'a string ' * 3.4
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Input In [32], in <cell line: 4>() 2 2 + 3.4 3 'a string ' * 3 ----> 4 'a string ' * 3.4 TypeError: can't multiply sequence by non-int of type 'float'
Type Operations
int + - / ** % // ...
float + - / * % // ...
string +
Variables¶
Used to store values and to assign them a name.
Examples:
i = 0counter = 5snpname = 'rs2315487'snplist = ['rs21354', 'rs214569']
In [33]:
width = 42
height = 20
snpname = 'rs56483 '
snplist = ['rs12345','rs458782']
snpname * 3
width * height
Out[33]:
840
How to correctly name a variable¶
Allowed: Not allowed:
Var_name 2save
_total *important
aReallyLongName Special%
with_digit_2 With spaces
dkfsjdsklut (well, allowed, but NOT recommended)
NO special characters:
+ - * $ % ; : , ? ! { } ( ) < > “ ‘ | \ / @
Summary¶
- Comment your code!
- Literals define values and can have different types (strings, integers, floats, boolean)
- Values can be collected in lists, tuples, sets, and dictionaries
- The operation that can be performed on a certain value depends on the type
- Variables are identified by a name and are used to store a value or collections of values
- Name your variables using descriptive words without special characters and reserved keywords
→ Notebook Day_1_Exercise_1 (~30 minutes)
NOTE!¶
How to get help?¶
- Google and Stack overflow are your best friends!
- Official python documentation
- Ask your neighbour
- Ask us
Python standard library¶
Python standard library¶
In [34]:
width = 5
height = 3.6
snps = ['rs123', 'rs5487']
snp = 'rs2546'
active = True
nums = [2,4,6,8,4,5,2]
int(height)
Out[34]:
3
More on operations¶
In [35]:
x = 4
y = 3
z = [2, 3, 6, 3, 9, 23]
pow(x, y)
Out[35]:
64
In [36]:
x = 5
y = 3
y != x
Out[36]:
True
In [37]:
x = 2
y = 3
x == 2 and y == 5
x = [2,4,7,3,5,9]
y = ['a','b','c']
2 in x
4 in x and 'd' in y
Out[37]:
False
In [38]:
# A simple loop that adds 2 to a number and checks if the number is even
i = 0
even = [2,4,6,8,10]
while i < 10:
num = i + 2
print('num is '+str(num)+'. Is this number even? '+str(num in even))
i += 1
num is 2. Is this number even? True num is 3. Is this number even? False num is 4. Is this number even? True num is 5. Is this number even? False num is 6. Is this number even? True num is 7. Is this number even? False num is 8. Is this number even? True num is 9. Is this number even? False num is 10. Is this number even? True num is 11. Is this number even? False
In [39]:
# A simple loop that adds 2 to a number, check if number is even and below 5
i = 0
even = [2,4,6,8,10]
while i < 10:
num = i + 2
print('num is '+str(num)+'. Is this number even and below 5? '+\
str(num in even and num < 5))
i += 1
num is 2. Is this number even and below 5? True num is 3. Is this number even and below 5? False num is 4. Is this number even and below 5? True num is 5. Is this number even and below 5? False num is 6. Is this number even and below 5? False num is 7. Is this number even and below 5? False num is 8. Is this number even and below 5? False num is 9. Is this number even and below 5? False num is 10. Is this number even and below 5? False num is 11. Is this number even and below 5? False
Word of caution when using operators¶
In [40]:
x = 5
y = 7
z = 2
x == 5 and y < 7 or z > 1
# and binds stronger than or
x > 4 or y == 6 and z > 3
x > 4 or (y == 6 and z > 3)
(x > 4 or y == 6) and z > 3
Out[40]:
False
In [41]:
# BEWARE!
x = 5
y = 8
#xx == 6 or xxx == 6 or x > 2
x > 42 and (xx > 1000 or y < 7)
Out[41]:
False
Python does short-circuit evaluation of operators
More on sequences (For example strings and lists)¶
Lists (and strings) are an ORDERED collection of elements where every element can be accessed through an index.
In [42]:
l = [2,3,4,5,3,7,5,9]
s = 'some longrandomstring'
#'o' in s
l[0]
s[4:7]
s[0:8:2]
s[-1]
l[0] = 42
s[0] = 'S'
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Input In [42], in <cell line: 10>() 8 s[-1] 9 l[0] = 42 ---> 10 s[0] = 'S' TypeError: 'str' object does not support item assignment
Mutable vs Immutable objects¶
Mutable objects can be altered after creation, while immutable objects can't.
Immutable objects: Mutable objects:
int•listfloat•setbool•dictstrtuple
Operations on mutable sequences¶
In [43]:
s = [0,1,2,3,4,5,6,7,8,9]
s.insert(5,10)
s.reverse()
s.append(10)
s
Out[43]:
[9, 8, 7, 6, 5, 10, 4, 3, 2, 1, 0, 10]
Summary¶
- The python standard library has many built-in functions regularly used
- Operators are used to carry out computations on different values
- Three types of operators; comparison, logical, and membership
- Order of precedence crucial!
- Mutable object can be changed after creation while immutable objects cannot be changed
→ Notebook Day_1_Exercise_2 (~30 minutes)
Loops in Python¶
In [44]:
fruits = ['apple','pear','banana','orange', 'grapes', 'pears']
print(fruits[0])
print(fruits[1])
print(fruits[2])
print(fruits[3])
print(fruits[4])
print(fruits[5])
apple pear banana orange grapes pears
In [45]:
fruits = ['apple','pear','banana','orange', 'grapes']
for fruit in fruits:
print(fruit)
print('DONE!')
apple pear banana orange grapes DONE!
Always remember to INDENT your loops!
Different types of loops¶
For loop¶
In [46]:
fruits = ['apple','pear','banana','orange']
mystring = 'mylongstring'
for fruit in fruits:
print(fruit)
apple pear banana orange
While loop¶
In [47]:
fruits = ['apple','pear','banana','orange']
i = 0
while i < len(fruits):
print(fruits[i])
i = i + 1
print(i)
apple pear banana orange 4
Different types of loops¶
For loop
Is a control flow statement that performs a fixed operation over a known amount of steps.
While loop
Is a control flow statement that allows code to be executed repeatedly based on a given Boolean condition.
Which one to use?
For loops better for simple iterations over lists and other iterable objects
While loops are more flexible and can iterate an unspecified number of times
→ Notebook Day_1_Exercise_3 (~20 minutes)
Conditional if/else statements
In [48]:
shopping_list = ['bread', 'egg', 'butter', 'milk']
if len(shopping_list) > 3:
print('Go shopping!')
Go shopping!
In [49]:
shopping_list = ['bread', 'egg', 'butter', 'milk']
tired = False
if len(shopping_list) > 5:
if not tired:
print('Go shopping!')
else:
print('Too tired, I\'ll do it later')
else:
if not tired:
print('Better get it over with today anyway')
else:
print('Nah! I\'ll do it tomorrow!')
Better get it over with today anyway
This is an example of a nested conditional¶
Putting everything into a Python script¶
Any longer pieces of code that have been used and will be re-used SHOULD be saved
Two options:
- Save it as a text file and make it executable
- Save it as a notebook file
Things to remember when working with scripts¶
- Put #!/usr/bin/env python in the beginning of the file
- Make the file executable to run with
./script.py - Otherwise run script with
python script.py
Working on files¶
In [50]:
fruits = ['apple','pear','banana','orange']
for fruit in fruits:
print(fruit)
apple pear banana orange
In [51]:
fh = open('../files/fruits.txt', 'r', encoding = 'utf-8')
for line in fh:
print(line)
fh.close()
apple pear banana orange
Aditional useful methods:¶
'string'.strip() Removes whitespace
'string'.split() Splits on whitespace into list
In [52]:
s = ' an example string to split with whitespace in end '
sw = s.strip()
sw
swl = sw.split()
swl = s.strip().split()
swl
Out[52]:
['an', 'example', 'string', 'to', 'split', 'with', 'whitespace', 'in', 'end']
In [53]:
fh = open('../files/fruits.txt', 'r', encoding = 'utf-8')
for line in fh:
print(line.strip())
fh.close()
apple pear banana orange
Another example¶
How much money is spent on ICA?
In [54]:
fh = open("../files/bank_statement.txt", "r", encoding = "utf-8")
total = 0
for line in fh:
expenses = line.strip().split() # split line into list
store = expenses[0] # save what store
price = float(expenses[1]) # save the price
if store == 'ICA': # only count the price if store is ICA
total = total + price
fh.close()
print('Total amount spent on ICA is: '+str(total))
Total amount spent on ICA is: 1186.71
Slightly more complex...¶
How much money is spent on ICA in September?
In [55]:
fh = open("../files/bank_statement_extended.txt", "r", encoding = "utf-8")
total = 0
for line in fh:
if not line.startswith('store'):
expenses = line.strip().split()
store = expenses[0]
year = expenses[1]
month = expenses[2]
day = expenses[3]
price = float(expenses[4])
if store == 'ICA' and month == '09': # store has to be ICA and month september
total = total + price
fh.close()
out = open("../files/bank_statement_results.txt", "w", encoding = "utf-8") # open a file for writing the results to
out.write('Total amount spent on ICA in september is: '+str(total))
out.close()
In [56]:
for file in os.scandir("../files/"):
print(time.ctime(os.stat(file).st_mtime), '\t', file.name)
Tue Oct 11 18:39:02 2022 250.imdb Thu May 20 17:46:00 2021 bank_statement.txt Thu May 20 17:46:00 2021 bank_statement_extended.txt Fri Oct 6 12:35:06 2023 bank_statement_results.txt Thu May 20 17:46:00 2021 blocket_listings_selected.txt Thu May 20 17:46:01 2021 cheat_sheet.pdf Thu May 20 17:46:01 2021 fruits.txt Thu May 20 17:46:01 2021 fruits_extended.txt Wed Oct 12 08:43:09 2022 imdb_reformatted.txt Fri Sep 30 15:40:44 2022 schedule.csv Thu May 20 17:46:01 2021 somerandomfile.txt
Summary¶
- Python has two types of loops,
Forloops andWhileloops - Loops can be used on any iterable types and objects
If/Elsestatement are used when deciding actions depending on a condition that evaluates to a boolean- Several
If/Elsestatements can be nested - Save code as notebook or text file to be run using python
- The function
open()can be used to read in text files - A text file is iterable, meaning it is possible to loop over the lines
→ Notebook Day_1_Exercise_4
Introduction to with Application to Bioinformatics - Day 1