-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
+
+
+
+
+
+
+
+
+Start by doing today's quiz
+Go to Canvas, Modules -> Day 4 -> Review Day 3
~20 minutes
+
+
+
+
+
+
+
+
+
+In what ways does the type of an object matter?¶
-
+
- Questions 1, 2 and 3 +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+row = 'sofa|2000|buy|Uppsala'
+fields = row.split('|')
+price = fields[1]
+if price == 2000:
+ print('The price is a number!')
+if price == '2000':
+ print('The price is a string!')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+print(sorted([ 2000, 30, 100 ]))
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+print(sorted(['2000', '30', '100']))
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+ord('2')
+
+
+
+
+
+
+
+
+
+In what ways does the type of an object matter?¶
-
+
Each type store a specific type of information
+-
+
intfor integers,
+floatfor floating point values (decimals),
+strfor strings,
+listfor lists,
+dictfor dictionaries.
+
+Each type supports different operations, functions and methods.
+
+
+
+
+
+
+
+
+
+
+-
+
- Each type supports different operations +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+30 > 2000
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+'30' > '2000'
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+30 > int('2000')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+'12345'[2]
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+12345[2]
+
+
+
+
+
+
+
+
+
+-
+
- Each type supports different functions +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+max('2000')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+max(2000)
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+math.cos(3.14)
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+math.cos('3.14')
+
+
+
+
+
+
+
+
+
+-
+
- Each type supports different methods +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+'ACTG'.lower()
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+[1, 2, 3].lower()
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+set([]).add('tiger')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+[].add('tiger')
+
+
+
+
+
+
+
+
+
+
+-
+
- How to find what methods are available: Python documentation, or
dir()
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+dir('ACTG') # list all attributes
+
+
+
+
+
+
+
+
+
+Convert string to number¶
-
+
- Questions 4, 5 and 6 +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+float('2000')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+float('0.5')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+float('1e9')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+float('1e-2')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+int('2000')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+int('1.5')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+int('1e9')
+
+
+
+
+
+
+
+
+Convert to boolean:
+Convert to boolean: 1, 0, '1', '0', '', {}¶
-
+
- Question 7 +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool(1)
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool(0)
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool('1')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool('0')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool('')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+bool({})
+
+
+
+
+
+
+
+
+
+-
+
- Python and the truth: true and false values +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+values = [1, 0, '', '0', '1', [], [0]]
+for x in values:
+ if x:
+ print(repr(x), 'is true!')
+ else:
+ print(repr(x), 'is false!')
+
+
+
+
+
+
+
+
+
+
+-
+
if xis equivalent toif bool(x)
+
+
+
+
+
+
+
+
+
+-
+
- Is
1equivalent toTrue?
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+1 == True
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+x = 1
+if x is True:
+ print(repr(x), 'is true!')
+else:
+ print(repr(x), 'is false!')
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+x = 1
+if bool(x) is True:
+ print(repr(x), 'is true!')
+else:
+ print(repr(x), 'is false!')
+
+
+
+
+
+
+
+
+
+
+-
+
- Be careful:
if x is Trueis not equivalent toif bool(x) is True
+
+
+
+
+
+
+
+
+
+Container types, when should you use which? (Question 8)¶
-
+
- lists: when order is important +
- dictionaries: to keep track of the relation between keys and values +
- sets: to check for membership. No order, no duplicates. +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+genre_list = ["comedy", "drama", "drama", "sci-fi"]
+genre_list
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+genres = set(genre_list)
+genres
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+'drama' in genre_list
+'drama' in genres
+# which operation is faster?
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+genre_counts = {"comedy": 1, "drama": 2, "sci-fi": 1}
+genre_counts
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+movie = {"rating": 10.0, "title": "Toy Story"}
+movie
+
+
+
+
+
+
+
+
+
+Python syntax (Question 9)¶
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+def echo(message): # starts a new function definition
+ # this function echos the message
+ print(message) # print state of the variable
+ return message # return the value to end the function
+
+
+
+
+
+
+
+
+
+Converting between strings and lists¶
-
+
- Question 10 +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+list("hello")
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+str(['h', 'e', 'l', 'l', 'o'])
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+'_'.join(['h', 'e', 'l', 'l', 'o'])
+
+
+
+
+
+
+
+
+
+What is a function?¶
-
+
- A named piece of code that performs a specific task +
- A relation (mapping) between inputs (arguments) and output (return value) +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+def increment_by_two(number):
+ number += 2
+ return number
+
+print(increment_by_two(100))
+
+
+
+
+
+
+
+
+
+TODAY¶
-
+
- More on functions:
-
+
- scop of variables +
- positional arguments and keyword arguments +
returnstatement
+
+ - Reusing code:
-
+
- comments and documentation +
- importing modules: using libraries +
+ - Pandas - explore your data! +
+
+
+
+
+
+
+
+
+More on functions: scope - global vs local variables¶
-
+
- Global variables can be accessed inside the function +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+HOST = 'global'
+
+def show_host():
+ print(f'HOST inside the function = {HOST}')
+
+show_host()
+print(f'HOST outside the function = {HOST}')
+
+
+
+
+
+
+
+
+
+-
+
- Change in the function will not change the global variable +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+HOST = 'global'
+
+def change_host():
+ HOST = 'local'
+ print(f'HOST inside the function = {HOST}')
+
+print(f'HOST outside the function before change = {HOST}')
+change_host()
+print(f'HOST outside the function after change = {HOST}')
+
+
+
+
+
+
+
+
+
+-
+
- Pass global variable as argument +
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+HOST = 'global'
+
+def change_host(HOST):
+ HOST = 'local'
+ print(f'HOST inside the function = {HOST}')
+
+print(f'HOST outside the function before change = {HOST}')
+change_host(HOST)
+print(f'HOST outside the function after change = {HOST}')
+
+
+
+
+
+
+
+
+
+More on functions: scope - global vs local variables cont.¶
List as global variables
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+MOVIES = ['Toy story', 'Home alone']
+
+def change_movie():
+ MOVIES = ['Fargo', 'The Usual Suspects']
+ print(f'MOVIES inside the function = {MOVIES}')
+
+print(f'MOVIES outside the function before change = {MOVIES}')
+change_movie()
+print(f'MOVIES outside the function after change = {MOVIES}')
+
+
+
+
+
+
+
+
+
+Will the global variable never to changed by function?
+
+
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+MOVIES = ['Toy story', 'Home alone']
+
+def change_movie():
+ MOVIES.extend(['Fargo', 'The Usual Suspects'])
+ print(f'MOVIES inside the function = {MOVIES}')
+
+print(f'MOVIES outside the function before change = {MOVIES}')
+change_movie()
+print(f'MOVIES outside the function after change = {MOVIES}')
+
+
+
+
+
+
+
+
+
+
+Take away: be careful when using global variables. Do not use it unless you know what you are doing.
+
+
+
+
+
+
+
+
+More on functions:
+More on functions: return statement¶
A function that counts the number of occurences of 'C' in the argument string.
+
+
+
+
+
+In [ ]:
+
+
+
+
+
+def cytosine_count(nucleotides):
+ count = 0
+ for x in nucleotides:
+ if x == 'c' or x == 'C':
+ count += 1
+ return count
+
+count1 = cytosine_count('CATATTAC')
+count2 = cytosine_count('tagtag')
+print(count1, count2)
+
-
-
-
Start by doing today's quiz
-Go to Canvas, Modules -> Day 4 -> Review Day 3
~20 minutes
+
+
+
+
-
+
+
-Functions that return are easier to repurpose than those that print their result
-
-
+
-
In what ways does the type of an object matter?¶
-
-
- Questions 1, 2 and 3 -
+
+
-
-
-
In [ ]:
-
-
-
-
row = 'sofa|2000|buy|Uppsala'
-fields = row.split('|')
-price = fields[1]
-if price == 2000:
- print('The price is a number!')
-if price == '2000':
- print('The price is a string!')
+
+In [ ]:
+
+
+cytosine_count('catattac') + cytosine_count('tactactac')
-
-
In [36]:
-
-
-
print(sorted([ 2000, 30, 100 ]))
+
+
+
-
+
+
+
In [ ]:
+
+
+
def print_cytosine_count(nucleotides):
+ count = 0
+ for x in nucleotides:
+ if x == 'c' or x == 'C':
+ count += 1
+ print(count)
+
+print_cytosine_count('CATATTAC')
+print_cytosine_count('tagtag')
-
-
In [ ]:
-
-
-
+
print(sorted(['2000', '30', '100']))
-
+
+
+
-
-
+
In [ ]:
+
+
-
+
print_cytosine_count('catattac') + print_cytosine_count('tactactac')
+
-
-
-
In what ways does the type of an object matter?¶
-
-
Each type store a specific type of information
--
-
intfor integers,
-floatfor floating point values (decimals),
-strfor strings,
-listfor lists,
-dictfor dictionaries.
-
-Each type supports different operations, functions and methods.
-
-
-
-
+
+
+
-
+
+
+
-
-
- Each type supports different operations +
- Functions without any
returnstatement returnsNone
-
-
In [ ]:
-
-
-
30 > 2000
+
+
+
-
+
+
+
In [ ]:
+
+
+
def foo():
+ do_nothing = 1
+
+r = foo()
+print(f'Return value of foo() = {r}')
-
-
In [ ]:
-
-
-
+
'30' > '2000'
-
+
+
+
+
-
+
+
-
+
- Use
returnfor all values that you might want to use later in your program
+
-
-
+
In [ ]:
-
-
-
+
30 > int('2000')
-
+
+
+
-
+
+
Keyword arguments¶
-
-
In [ ]:
-
-
-
'12345'[2]
+
+
+
-
+
+
+
In [ ]:
+
+
+
fh = open('files/recipes.txt', mode='w', encoding='utf-8')
-
-
In [ ]:
-
-
-
-
12345[2]
+
+
+
+
+
+
+In [ ]:
+
+
+
sorted([1, 4, 100, 5, 6], reverse=True)
-
-
-
-
-
- Each type supports different functions -
+
+
+
-
+
+
Why do we use keyword arguments?¶
-
-
In [ ]:
-
-
-
+
max('2000')
+
+
+
-
+
+
+
In [ ]:
+
+
+
record = 'gene_id INSR "insulin receptor"'
+
+record.split(' ', 2)
-
-
In [ ]:
-
-
-
max(2000)
+
+
+
-
+
+
+
In [ ]:
+
+
+
record.split(sep=' ', maxsplit=2)
-
-
In [ ]:
-
-
+
-
math.cos(3.14)
+
+
+
+
+
+
+
+
+
+
+-
+
- It increases the clarity and redability +
+
+
+
+
+
+
+
+
+The order of keyword arguments does not matter¶
+
+
+
-
+
+
+
In [ ]:
+
+
+
fh = open('files/recipes.txt', mode='w', encoding='utf-8'); fh.close()
-
-
In [ ]:
-
-
-
-
math.cos('3.14')
+
+
+
+
+
+
+In [ ]:
+
+
+
fh = open('files/recipes.txt', encoding='utf-8', mode='w'); fh.close()
-
-
-
-
-
- Each type supports different methods +
- if there is no ambiguity
- How to find what methods are available: Python documentation, or
dir()
+ - Positional arguments must be in front of keyword arguments
- Questions 4, 5 and 6 -
- arguments before
/must be specified with position
+ - arguments after
*must be specified with keyword
+ - Just define them as usual: +
- Question 7 +
- Convention: use the object
None - Default value for optional arguments +
- Implicit return value of functions without a
returnstatement
+ NoneisNone, not anything else
+- Python and the truth: true and false values -
if xis equivalent toif bool(x)
-- Notebook Day_4_Exercise_1 (~30 minutes) +
- Go to Canvas,
Modules -> Day 4 -> Exercise 1 - day 4
+ Quiz. Go to Canvas,
+Modules -> Day 4 -> PyQuiz 4.1
+Lunch break
+
+Extra reading:
-
-
- Is
1equivalent toTrue?
+ - https://realpython.com/python-kwargs-and-args/ +
- https://able.bio/rhett/python-functions-and-best-practices--78aclaa +
- Is
- Functions
-
+
- e.g. sum(), print(), open() +
+ - Modules
-
+
- files containing a collection of functions and methods, e.g. string.py +
+ - Documentation
-
+
- docstring, comments +
+ - Cleaner code +
- Better defined tasks in code +
- Re-usability +
- Better structure +
- Be careful:
if x is Trueis not equivalent toif bool(x) is True
- - lists: when order is important -
- dictionaries: to keep track of the relation between keys and values -
- sets: to check for membership. No order, no duplicates. +
- Cleaner code +
- Better defined tasks in code +
- Re-usability +
- Better structure
- Collect all related functions in one file +
- Import a module to use its functions +
- Only need to understand what the functions do, not how +
+
+
-
+
+
+
+
Can be used in both ways, with or without keyword¶
-
+
-
-
In [ ]:
-
-
-
'ACTG'.lower()
+
+
+
-
+
+
+
In [ ]:
+
+
+
fh = open('files/recipes.txt', 'w', encoding='utf-8'); fh.close()
-
-
In [ ]:
-
-
-
[1, 2, 3].lower()
+
+
+
-
+
+
+
In [ ]:
+
+
+
fh = open('files/recipes.txt', mode='w', encoding='utf-8'); fh.close()
-
-
In [ ]:
-
-
+
-
+
set([]).add('tiger')
-
+
+
+
-
+
+
But there are some exceptions¶
-
-
In [ ]:
-
-
-
[].add('tiger')
+
+
+
+
+
+
+In [ ]:
+
+
+
fh = open('files/recipes.txt', encoding='utf-8', 'w'); fh.close()
-
-
-
+
+
+
-
+
+
+
-
-
-
+
-
In [ ]:
-
-
-
-
+dir('ACTG') # list all attributes
-
+
-
+
+
+
+
-Restrictions by purpose¶
-
-
+
-
Convert string to number¶
-
-
+
+
-
-
-
In [ ]:
-
-
-
-
float('2000')
+
+In [ ]:
+
+
+sorted([1, 4, 100, 5, 6], reverse=True)
-
-
In [ ]:
-
-
-
float('0.5')
+
+
+
-
+
+
+
In [ ]:
+
+
+
sorted([1, 4, 100, 5, 6], True)
-
-
In [ ]:
-
-
-
float('1e9')
+
+
+
-
+
+
+
In [ ]:
+
+
+
sorted(iterable, /, *, key=None, reverse=False)
-
-
In [ ]:
-
-
-
+float('1e-2')
-
+
+
+
-
+
+
-
+
-
+
-
In [ ]:
-
-
-
+
+int('2000')
-
+
+
+
+
+
+
+
How to define functions taking keyword arguments¶
-
+
+
+
-
-
-
In [ ]:
-
-
-
-
int('1.5')
+
+In [ ]:
+
+
+def format_sentence(subject, value, end):
+ return 'The ' + subject + ' is ' + value + end
+
+print(format_sentence('lecture', 'ongoing', '.'))
+
+print(format_sentence('lecture', 'ongoing', end='!'))
+
+print(format_sentence(subject='lecture', value='ongoing', end='...'))
-
-
In [ ]:
-
-
-
+
-
int('1e9')
+
+
+
+
+
+
+
+
+
+Defining functions with default arguments¶
+
+
+
+
+
+
+In [ ]:
+
+
+
def format_sentence(subject, value, end='.'):
+ return 'The ' + subject + ' is ' + value + end
+
+print(format_sentence('lecture', 'ongoing'))
+
+print(format_sentence('lecture', 'ongoing', '...'))
-
-
-Convert to boolean:
Convert to boolean: 1, 0, '1', '0', '', {}¶
-
-
+
+
-
+
+
+
+
Defining functions with optional arguments¶
-
+
-
-
In [ ]:
-
-
-
bool(1)
+
+
+
-
+
+
+
In [ ]:
+
+
+
def format_sentence(subject, value, end='.', second_value=None):
+ if second_value is None:
+ return 'The ' + subject + ' is ' + value + end
+ else:
+ return 'The ' + subject + ' is ' + value + ' and ' + second_value + end
+
+print(format_sentence('lecture', 'ongoing'))
+
+print(format_sentence('lecture', 'ongoing',
+ second_value='self-referential', end='!'))
-
-
In [ ]:
-
-
+
-
+
bool(0)
-
+
+
+
+
+
+
+Small detour: Python's value for missing values:
Small detour: Python's value for missing values: None¶
-
+
+
+
-
-
-
In [ ]:
-
-
-
-
bool('1')
+
+In [ ]:
+
+
+None == 0
-
-
In [ ]:
-
-
-
bool('0')
+
+
+
-
+
+
+
In [ ]:
+
+
+
None == False
-
-
In [ ]:
-
-
-
bool('')
+
+
+
-
+
+
+
In [ ]:
+
+
+
None == ''
-
-
In [ ]:
-
-
-
+
bool({})
-
+
+
+
-
+
In [ ]:
+
+
-
+
bool(None)
+
-
-
+
-
-
-
+
+
-
-
-
In [ ]:
-
-
-
values = [1, 0, '', '0', '1', [], [0]]
-for x in values:
- if x:
- print(repr(x), 'is true!')
- else:
- print(repr(x), 'is false!')
+
+In [ ]:
+
+
+type(None)
-
-
+
-
-
-
-
+-
-
+
+
-
-
-
+
-
+
+
Exercise 1¶
-
+
-
-
-
-In [ ]:
-
-
-
-
-
-1 == True
-
-
-
In [ ]:
-
-
+
-
+
x = 1
-if x is True:
- print(repr(x), 'is true!')
-else:
- print(repr(x), 'is false!')
-
+
+
+
-
+
+
A short note on code structure¶
-
+
-
-
In [ ]:
-
-
+
-
+
x = 1
-if bool(x) is True:
- print(repr(x), 'is true!')
-else:
- print(repr(x), 'is false!')
-
+
+
+
-
+
+
Why functions?¶
-
+
-
+
-
-
-
-
+-
-
+
+
-
-
-
-
-Container types, when should you use which? (Question 8)¶
-
-
+
+
Why modules?¶
-
+
-
-
In [43]:
-
-
-
+
genre_list = ["comedy", "drama", "drama", "sci-fi"]
-genre_list
-
+
+
+
+
-
+
+
-
+
-
-
+
In [44]:
-
-
-
+
genres = set(genre_list)
-genres
-
+
+
+
-
+
+
Example of modules¶
-
-
In [45]:
-
-
-