Introduction to¶

with Application to Bioinformatics¶

- Day 1¶

Who we are¶

Nina	Dimitris	Dan	Jeanette	Ingrid

John	Rui	Kristina	Claudio

Who you are¶

Drawing

Practical issues¶

Course website: https://nbisweden.github.io/workshop-python/ht20/
One main room for lectures
Same room is used for questions during exercises
Try to keep your cameras on, but microphone muted
Breakout rooms are used for discussions in smaller groups, a TA will be assigned to each group
HackMD used for interaction and questions
Short lectures with many breaks

Practical issues¶

During exercises, TRY TO DISCONNECT FROM ZOOM. You can always connect when you have a question
Take lots of small breaks also when working with the exercises
We will try to stick to the schedule, but it's only preliminary until it's happened

If you have any questions during the lecture, feel free to unmute and ask. If you don't want to ask in the Zoom meeting, write the question in the HackMD

To start with¶

Write a short presentation of yourself in the HackMD

Schedule¶

Drawing

Check¶

Has everyone managed to install Python?
Have you managed to run the test script?
Have you installed notebooks? (optional)

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!

Why Python?¶

Typical workflow¶

Get data
Clean, transform data in spreadsheet
Copy-paste, copy-paste, copy-paste
Run analysis & export results
Realise the columns were not sorted correctly
Go back to step 2, Repeat

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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 2.4 - November 30, 2004
Python 2.5 - September 19, 2006
Python 2.6 - October 1, 2008
Python 2.7 - July 3, 2010

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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:

Google
Ask your neighbour
Ask an assistant

Day 1¶

Types and variables
Operations
Loops
if/else statements

Example of a simple Python script¶

In [1]:

# A simple loop that adds 2 to a number
i = 0
while i < 10:
    u = i + 2
    print('u is',u)
    i += 1

u is 2
u is 3
u is 4
u is 5
u is 6
u is 7
u is 8
u is 9
u is 10
u is 11

Example of a simple Python script¶

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Comment¶

All lines starting with # is interpreted by python as a comment and are not executed. Comments are important for documenting code and considered good practise when doing all types of programming

Example of a simple Python script¶

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Literals¶

All literals have a type:

Strings (str) ‘Hello’ “Hi”
Integers (int) 5
Floats (float) 3.14
Boolean (bool) True or False

Literals define values¶

In [6]:

'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('this is a string')

Out[6]:

str

Collections¶

In [7]:

[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[7]:

list

What operations can we do with different values?¶

That depends on their type:

In [9]:

'a string'+' another string'
#2 + 3.4
#'a string ' * 3.2

Out[9]:

'a string another string'

Type Operations

int + - / ** % // ...
float + - / * % // ...
string +

Example of a simple Python script¶

Drawing

Identifiers¶

Identifiers are used to identify a program element in the code.

For example:

Variables
Functions
Modules
Classes

Variables¶

Used to store values and to assign them a name.

Examples:

i = 0
counter = 5
snpname = 'rs2315487'
snplist = ['rs21354', 'rs214569']

In [12]:

width  = 23564
height = 10

snpname = 'rs56483 '
snplist = ['rs12345','rs458782']

width * height

Out[12]:

How to correctly name a variable¶

Drawing

Allowed: Not allowed:
Var_name 2save
_total *important
aReallyLongName Special%
with_digit_2 With spaces
dkfsjdsklut (well, allowed, but NOT recommended)

NO special characters:
+ - * $ % ; : , ? ! { } ( ) < > “ ‘ | \ / @

Reserved keywords¶

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These words can not be used as variable names

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¶

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Example `print()` and `str()`¶

Drawing

Note!
Here we format everything to a string before printing it

Python standard library¶

Drawing

In [39]:

width  = 5
height = 3.6
snps   = ['rs123', 'rs5487']
snp    = 'rs2546'
active = True
nums   = [2,4,6,8,4,5,2]

float(width)

Out[39]:

5.0

More on operations¶

Drawing

In [40]:

x = 4
y = 3
z = [2, 3, 6, 3, 9, 23]
pow(x, y)

Out[40]:

Comparison operators¶

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Can be used on int, float, str, and bool. Outputs a boolean.

In [41]:

x = 5
y = 3

#x = 5.14
#y = 3.14

y != x

Out[41]:

True

Logical operators¶

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Membership operators¶

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In [42]:

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[42]:

False

In [13]:

# 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:
    u = i + 2
    print('u is '+str(u)+'. Is this number even? '+str(u in even))
    i += 1

u is 2. Is this number even? True
u is 3. Is this number even? False
u is 4. Is this number even? True
u is 5. Is this number even? False
u is 6. Is this number even? True
u is 7. Is this number even? False
u is 8. Is this number even? True
u is 9. Is this number even? False
u is 10. Is this number even? True
u is 11. Is this number even? False

In [14]:

# 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:
    u = i + 2
    print('u is '+str(u)+'. Is this number even and below 5? '+\
          str(u in even and u < 5))
    i += 1

u is 2. Is this number even and below 5? True
u is 3. Is this number even and below 5? False
u is 4. Is this number even and below 5? True
u is 5. Is this number even and below 5? False
u is 6. Is this number even and below 5? False
u is 7. Is this number even and below 5? False
u is 8. Is this number even and below 5? False
u is 9. Is this number even and below 5? False
u is 10. Is this number even and below 5? False
u is 11. Is this number even and below 5? False

Order of precedence¶

There is an order of precedence for all operators:

Drawing

Word of caution when using operators¶

In [43]:

x = 5
y = 7
z = 2
(x > 6 and y == 7) or z > 1

x > 6 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[43]:

False

In [44]:

# BEWARE!
x = 5
y = 8

#xx == 6 or xxx == 6 or x > 2
x > 42 or (y < 8 and someRandomVariable > 1000)

Out[44]:

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.

Drawing

In [47]:

l = [2,3,4,5,3,7,5,9]
s = 'some longrandomstring'

'o' in s

l[1]
s[0:7]
s[0:8:2]
s[-2]
l[0] = 42
s[0] = 'S'

Mutable vs Immutable objects¶

Mutable objects can be altered after creation, while immutable objects can't.

Immutable objects: Mutable objects:

int • list
float • set
bool • dict
str
tuple

Operations on mutable sequences¶

Drawing

In [48]:

s = [0,1,2,3,4,5,6,7,8,9]
s.insert(5,10)
s.reverse()
s

Out[48]:

[9, 8, 7, 6, 5, 10, 4, 3, 2, 1, 0]

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 [26]:

fruits = ['apple','pear','banana','orange']

print(fruits[0])
print(fruits[1])
print(fruits[2])
print(fruits[3])

apple
pear
banana
orange

In [27]:

fruits = ['apple','pear','banana','orange']

for fruit in fruits:
    print(fruit)
#    print('end')
print('end')

apple
pear
banana
orange
end

Always remember to INDENT your loops!

Different types of loops¶

`For` loop¶

In [49]:

fruits = ['apple','pear','banana','orange']

for fruit in fruits:
    print(fruit)
print('end')

apple
pear
banana
orange
end

`While` loop¶

In [51]:

fruits = ['apple','pear','banana','orange']

i = 0
while i < len(fruits):
    print(fruits[i])
    i = i + 1

apple
pear
banana
orange

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

Example of a simple Python script¶

Drawing

→ Notebook Day_1_Exercise_3 (~20 minutes)

Conditional `if/else` statements

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In [52]:

shopping_list = ['bread', 'egg', 'butter', 'milk']

if len(shopping_list) > 5:
    print('Go shopping!')
else:
    print('Nah! I\'ll do it tomorrow!')

Nah! I'll do it tomorrow!

In [53]:

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

Examples

Things to remember when working with scripts¶

Put #!/usr/bin/env python3 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 [54]:

fruits = ['apple','pear','banana','orange']

for fruit in fruits:
    print(fruit)

apple
pear
banana
orange

Drawing

In [55]:

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 [56]:

s  = '  an example string to split with whitespace in end   '
sw = s.strip()
sw
#l  = sw.split()
#l
#l  = s.strip().split('\t')
#l

Out[56]:

'an example string to split with whitespace in end'

Drawing

In [36]:

fh = open('../files/fruits.txt', 'r', encoding = 'utf-8')

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

fh.close()

apple
pear
banana
orange

Another example¶

Drawing How much money is spent on ICA?

In [57]:

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...¶

Drawing

How much money is spent on ICA in September?

In [ ]:

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()

Summary¶

Python has two types of loops, For loops and While loops
Loops can be used on any iterable types and objects
If/Else statement are used when deciding actions depending on a condition that evaluates to a boolean
Several If/Else statements 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¶

Who we are¶

Who you are¶

Practical issues¶

Practical issues¶

To start with¶

Schedule¶

Check¶

What is programming?¶

What can we use it for?¶

Why Python?¶

Typical workflow¶

Python versions¶

Some good advice¶

Day 1¶

Example of a simple Python script¶

Example of a simple Python script¶

Comment¶

Example of a simple Python script¶

Literals¶

Literals define values¶

Collections¶

What operations can we do with different values?¶

Example of a simple Python script¶

Identifiers¶

Variables¶

How to correctly name a variable¶

Reserved keywords¶

Summary¶

NOTE!¶

How to get help?¶

Python standard library¶

Example print() and str()¶

Python standard library¶

More on operations¶

Comparison operators¶

Logical operators¶

Membership operators¶

Order of precedence¶

Word of caution when using operators¶

More on sequences (For example strings and lists)¶

Mutable vs Immutable objects¶

Operations on mutable sequences¶

Summary¶

Loops in Python¶

Different types of loops¶

For loop¶

While loop¶

Different types of loops¶

Example of a simple Python script¶

Conditional if/else statements

This is an example of a nested conditional¶

Putting everything into a Python script¶

Things to remember when working with scripts¶

Working on files¶

Aditional useful methods:¶

Another example¶

Slightly more complex...¶

Summary¶

Example `print()` and `str()`¶

`For` loop¶

`While` loop¶

Conditional `if/else` statements