Python 101: for biologists, by biologists

Arithmetic operators

+ Addition
- Subtraction
* Multiplication
** Exponent
/ Division
// Floor Division
% Modulus

Arithmetic examples: + - * /

#
print 2 + 2
print 4 - 2
print 2 * 4
print 8 / 2
print 2 * 3 + 3 * 2
print (2 * 3) + (3 * 2)
print 2 * (3 + 3) * 2

Arithmetic examples: / //

#
print 8 / 3
print 8.0 / 3
print 8.0 // 3
2<br />2.6666666666666665<br />2 #forceoutput

Arithmetic examples: ** and operators style

#
print 2 ** 4
print 2**4
print 2 **4
print 2** 4

PEP 8 -- Style Guide for Python Code

Arithmetic examples

#
print 8.0 / 3
print 8. / 3

Arithmetic examples

#
print 5.0 / 3
print 5.0 // 3
print 5.0 % 3

Variables

"...a variable is a storage location and an associated symbolic name..." in Wikipedia

Assignment statement

#
a = 1
print a

This is different from the equal operator ==

#
a = 1
print a == 1
print a == 2

Variables usefulness

#
print "Interesting genes number: "
print 15
print "Uninteresting genes number"
print 30
print "Total genes: "
print 15 + 30

Variables usefulness

#
igenes = 15 # Interesting genes
ugenes = 30 # Uninteresting genes
print "Interesting genes number: "
print igenes
print "Uninteresting genes number: "
print ugenes
print "Total genes: "
print igenes + ugenes

Variables forbidden names

The following identifiers are used as reserved words, or keywords of the language, and cannot be used as ordinary identifiers.

and       del       from      not       while
as        elif      global    or        with
assert    else      if        pass      yield
break     except    import    print     None
class     exec      in        raise     _*
continue  finally   is        return    __*__
def       for       lambda    try       __*

More information

Python Documentation: Identifiers

Assignment operators

= Simple assignment operator
+= Add AND assignment operator
-= Subtract AND assignment operator
*= Multiply AND assignment operator
/= Divide AND assignment operator
//= Floor Dividion and assigns a value
%= Modulus AND assignment operator
**= Exponent AND assignment operator

Assignment examples

#
a = 1
a = a + 3
print a

#
a = 1
a += 3
print a

Assignment examples

#
counter = 0
 # Do something and increment counter
counter += 1
 # Repeat something in a loop and increment counter each time
counter += 1
 # Check expected counter number reached and stop working
print counter

Assignment examples

#
a = 2
a *= 20; print a
a /= 3; print a
a //= 2; print a
a %= 4; print a
a **= 6; print a

Data types

Numbers (integers and floats)
Strings
Lists
Tuples
Sets
Dictionaries

More information

Python Documentation

Integers and floats

Numbers are created by numeric literals or as the result of built-in functions and operators
Numeric literals containing a decimal point or an exponent sign yield floating point numbers
Python fully supports mixed arithmetic

Integers and floats assignment

#
a = 1
b = 2.0
print a + b

Strings

String literals are written in single or double quotes
In triple-quoted strings, unescaped newlines and quotes are allowed (and are retained)
Strings are immutable sequence types: such objects cannot be modified once created

Strings assignment

#
a = "hello"
b = "world"
print a + b

Strings assignment

Please try the following lines in the editor below

print "hello world"
print 'hello world'
print 'hello" "world'
print "hello' 'world"
print 'hello"
print "world'

#
print "hello world"

Strings assignment multiline

""" or '''

#
seq = """ABCD
EFGH
IJKLMNOPQ"""
print seq

Integers + Strings

#
a = 1
b = "hello"
print a + b

Integers * Strings

#
a = 5
b = "hello "
print a * b

Strings slices

variable = "string"
variable[start:stop:step]

#
seq = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print seq[1:5]

Strings slices

#
seq = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print seq[:]
print seq[0]
print seq[0:5]
print seq[:5]
print seq[5:]

Strings slices with negative indices

#
seq = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print seq[-1]
print seq[-5:-1]
print seq[-0]

Strings slices with steps

#
seq = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print seq[0:10:2]
print seq[-1:-11:-2]
print seq[:-11:-1]
print seq[::-1] # This one is very useful
print seq[::-2]

Strings slices out of range

#
seq = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
print seq[5:100]

Strings methods

capitalize center count decode encode endswith expandtabs find format index isalnum isalpha isdigit islower isspace istitle isupper join ljust lower lstrip partition replace rfind rindex rjust rpartition rsplit rstrip split splitlines startswith strip swapcase title translate upper zfill

Total: 38

CHALLENGE FAILED

Strings methods

count endswith find islower isupper join lower lstrip replace rfind rsplit rstrip split splitlines startswith strip swapcase translate upper

Total: 19

CHALLENGE CONSIDERED

Strings methods

count
find
replace
startswith and endswith
islower and isupper
lower, upper and swapcase
join
strip
translate
split and splitlines ← later with Lists

Total: 10

Strings methods

More information

Python Documentation

String count

str.count(sub[, start[, end]])

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.count("A")

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.count("A", 0 , 10)
2 #forceoutput

String replace

str.replace(old, new[, count])

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.replace("T", "U")

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.replace("T", "U", 3)
UCCUGGAGGAGAAUGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA #forceoutput

String translate

str.translate(table[, deletechars])
string.maketrans(from, to)

#
seq = "TCCTGGAGGAGAATGGAGGTCGAGANNNNNGGTGTGGTGGGGGTGANNNNN"
print seq.translate(None, "AT")
CCGGGGGGGGGCGGGCCGCGGGGGGGGGGGGGGGG #forceoutput

#
import string # We'll learn about this line later
seq = "TCCTGGAGGAGAATGGAGGTCGAGANNNNNGGTGTGGTGGGGGTGANNNNN"
table = string.maketrans("AGTC", "1234")
print seq.translate(table, "N")
34432212212113221223421212232322322222321 #forceoutput

String startswith and endswith

str.startswith(suffix[, start[, end]])

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.startswith("TCCT")
print seq.startswith("TGCT")
print seq.startswith("ATG", 12, 20)
True<br />False<br />True #forceoutput

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.endswith("TGA")
True #forceoutput

String find and rfind

str.find(sub[, start[, end]])

#
seq = "TCCTGGAGGAGAATGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.find("GTC")
print seq.rfind("GTC")

#
seq = "TCCTGGAGGAGGTCAAGGGTCCAGCTGGAGAAGTTTAGGGTGTGGTGGGGGTGA"
print seq.find("ATG", 0, 10)
-1 #forceoutput

String islower and isupper

str.islower()

#
a = "T"
cod1 = "ATG"
cod2 = "AtG"
print a.isupper()
print cod1.isupper()
print cod2.isupper()
True<br />True<br />False<br /> #forceoutput

String lower, upper and swapcase

str.lower()

#
cod = "AtG"
print cod.lower()
print cod.upper()

#
cod = "AtG"
print cod.swapcase()
aTg #forceoutput

String join

str.join(iterable)

#
str = "TCCTGG"
print ":".join(str)

String strip, lstrip and rstrip

str.strip([chars])

#
seq = "NNNNGCGCGCTGGAGGAGGTGAGAAGTTTAGGGTAAAAAAAAANNNN"
seq = seq.strip("N")
print seq
print seq.lstrip("GC")
print seq.rstrip("A")
print seq.strip("ATG")
GCGCGCTGGAGGAGGTGAGAAGTTTAGGGTAAAAAAAAA<br />TGGAGGAGGTGAGAAGTTTAGGGTAAAAAAAAA<br />GCGCGCTGGAGGAGGTGAGAAGTTTAGGGT<br />CGCGC #forceoutput

Data Structures

Numbers
Strings
Lists
Tuples
Sets
Dicts

Lists

List of objects (Duh!)
Mutable sequence type (allow in-place modification of the object)

Lists assignment

[a, b, c]

#
a = []
b = [1,2,3,4,5]
c = ["a", "b", "c", "d", "f"]
print a
print b[0]
print c[-1]

Lists assignment

#
a = [0] * 5
b = [1] * 5
c = ['NA'] * 5
d = range(5) # range([start], stop[, step]) [1]
print a
print b
print c
print d

[1] Python Built-in Functions

Lists assignment

str.split([sep[, maxsplit]])

#
raw_data = "TCCTGGAGGAG;GTCAAGGGTCCAGCT;GGAGAAGTTTAGGG;TGTGGTG;GGGGTGA"
sequences = raw_data.split(";")
print sequences

#
raw_data = "TCCTGGAGGAG;GTCAAGGGTCCAGCT;GGAGAAGTTTAGGG;TGTGGTG;GGGGTGA"
sequences = raw_data.split(";", 3)
['TCCTGGAGGAG', 'GTCAAGGGTCCAGCT', 'GGAGAAGTTTAGGG;TGTGGTG;GGGGTGA'] #forceoutput

Lists assignment

str.splitlines([keepends])

#
raw_data = """TCCTGGAGGAG
GTCAAGGGTCCAGCT
GGAGAAGTTTAGGG"""
sequences = raw_data.splitlines()
['TCCTGGAGGAG', 'GTCAAGGGTCCAGCT', 'GGAGAAGTTTAGGG'] #forceoutput

Lists assignment

str.splitlines([keepends])

#
raw_data = """TCCTGGAGGAG
GTCAAGGGTCCAGCT
GGAGAAGTTTAGGG"""
sequences = raw_data.splitlines(True)
['TCCTGGAGGAG\n', 'GTCAAGGGTCCAGCT\n', 'GGAGAAGTTTAGGG'] #forceoutput

Lists are a mutable sequence type

#
mylist = ["A", "T", "G", "C"]
print mylist[0]
mylist[0] = "T"
print mylist

#
myseq = "ATGC"
print myseq[0]

Multi-dimensional lists

#
mylist = [["A", "T", "G", "C"], [1, 2, 3, 4]]
print mylist
print mylist[0]
print mylist[1][2]

Lists methods

count
index
append
insert
remove
pop
reverse
sort

More information

Python Documentation

Lists count, index, append and insert

#
mylist = ["A", "T", "G", "C", "A", "T"]
print mylist.count("A")
print mylist.index("C")
mylist.append("TAIL")
mylist.insert(3, "MIDDLE")
print mylist

Lists remove

#
mylist = ["A", "T", "G", "C", "A", "T"]
mylist.remove("A")
print mylist
mylist.remove("A")
print mylist

Lists pop

#
mylist = ["A", "T", "G", "C", "A", "T"]
mylist.pop(2)
print mylist
print mylist.pop(1)
print mylist

Lists reverse and sort

#
mylist = [1, 1, 3, 5, 2, 4]
mylist.sort()
print mylist
mylist.reverse()
print mylist

Lists with Python Built-in Functions

#
mylist=range(5)
print mylist
print len(mylist)
print min(mylist)
print max(mylist)

More information

Python Documentation

Lists with join

#
mylist = ["A", "T", "G", "C", "A", "T"]
print "".join(mylist)

Data Structures

Numbers
Strings
Lists
Tuples
Sets
Dicts

Tuples

Lists that are immutable (like strings)
Useful for storing heterogeneous data in which order has semantic value (like coordinates)
Fast!!!

More information

Python Docs: Tuples and Sequences

Tuples assignment

#
coord1 = 12, 35 # pair of coordinates
coord2 = (32, 12)
coordinates = [coord1, coord2]
print coordinates

Data Structures

Numbers
Strings
Lists
Tuples
Sets
Dicts

Sets

Unordered collection with no duplicate elements
Uses include membership testing and eliminating duplicate entries
Also support mathematical operations like union, intersection, difference, and symmetric difference.

More information

Python Docs: Sets

Sets

#
palette = set(['blue', 'red', 'green', 'red'])
print "blue" in palette
print "magenta" in palette

Sets

#
p1 = set(['blue', 'red', 'green', 'red'])
p2 = set(['yellow', 'green', 'blue', 'yellow', 'blue'])
print p1 - p2 # colors in p1 but not in p2
print p1 | p2 # colors in either p1 or p2
print p1 & p2 # colors in both p1 and p2
print p1 ^ p2 # colors in p1 or p2 but not both
set(['red'])<br />set(['blue', 'green', 'yellow', 'red'])<br />set(['blue', 'green'])<br />set(['red', 'yellow']) #forceoutput

Data Structures

Numbers
Strings
Lists
Tuples
Sets
Dicts

Dictionaries

Unordered set of "key: value" pairs, with the requirement that the keys are unique
Known in other languages as "associative memories" or "associative arrays"
Indexed by keys (unlike sequences, which are indexed by a range of numbers)
Indices can be any immutable type (strings, numbers, or tuples of immutable objects)
Usefull for storing, extracting or deleting values with a key

Dictionaries assignment

{'a': 1, 'b': 2, 'c': 3}
{'key1': "Value", 'key2': "Value", 1: "Another Value", 'd': 42}

#
sequences = {'s1': "AGTAGCGT", 's2': "ATGAC", 'primer': "AGCTGCTAG"}
print sequences['primer']
del sequences['s2']
print sequences

Dictionaries assignment

#
sequences = {'s1': "AGTAGCGT", 's2': "ATGAC", 'primer': "AGCTGCTAG"}
sequences['s1'] = "AAAAAAAA"
print sequences
print sequences.items()
print sequences.keys()
print sequences.values()
print 'primer' in sequences

Wrap up

Arithmetic operators + - * / // % **
Assignment operators += -= *= /= //= %= **=
Numbers and Strings a = 1; b = "Hello World"
String methods count, find, join, translate, split, etc
Lists and methods a = [1, 2]; append, pop, reverse, sort, etc
Some Built-in functions range, len, min, max
Tuples a = 1, 2, 3; b = (1, 2, 3)
Sets a = set([1, 2, 3])
Dictionaries a = {a: 1, b: 2, c: 3}

Python 101

Data Structures

Overview

Arithmetic operators

Arithmetic examples: + - * /

Arithmetic examples: / //

Arithmetic examples: ** and operators style

Arithmetic examples

Arithmetic examples

Variables

Assignment statement

Variables usefulness

Variables usefulness

Variables forbidden names

More information

Assignment operators

Assignment examples

Assignment examples

Assignment examples

Data types

More information

Integers and floats

Integers and floats assignment

Strings

Strings assignment

Strings assignment

Please try the following lines in the editor below

Strings assignment multiline

Integers + Strings

Integers * Strings

Strings slices

Strings slices

Strings slices with negative indices

Strings slices with steps

Strings slices out of range

Strings methods

Strings methods

Total: 38

Strings methods

Total: 19

Strings methods

Total: 10

Strings methods

More information

String count

String replace

String translate

String startswith and endswith

String find and rfind

String islower and isupper

String lower, upper and swapcase

String join

String strip, lstrip and rstrip

Data Structures

Lists

Lists assignment

Lists assignment

[1] Python Built-in Functions

Lists assignment

Lists assignment

Lists assignment

Lists are a mutable sequence type

Multi-dimensional lists

Lists methods

More information

Lists count, index, append and insert

Lists remove

Lists pop

Lists reverse and sort

Lists with Python Built-in Functions

More information

Lists with join

Data Structures

Tuples

More information

Tuples assignment

Data Structures

Sets

More information

Sets