This document contains a dictionary that maps nucleotide sequences to amino acids. It defines the genetic code by listing the 3-letter codon sequences and their corresponding single-letter amino acid abbreviations. The document also contains some example nucleotide sequences and a prompt to find the answer in the file ultimate-sequence.txt.

2. FBW
03-10-2017
Wim Van Criekinge

3. Google Calendar
Louis Coussement

4. Bioinformatics.be

5. Overview
What is Python ?
Why Python 4 Bioinformatics ?
How to Python
IDE: Eclipse & PyDev / Athena
Code Sharing: Git(hub)
Strings
Regular expressions

6. Version 2.7 and 3.6 on athena.ugent.be

7. GitHub: Hosted GIT
• Largest open source git hosting site
• Public and private options
• User-centric rather than project-centric
• http://github.ugent.be (use your Ugent
login and password)
• URI (also on minerva)
– https://github.ugent.be/wvcrieki/Bioinfo
rmatics_2017.py.git

8. Control Structures
if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue

9. range
 The range function specifies a range of integers:
 range(start, stop) - the integers between start (inclusive)
and stop (exclusive)
 It can also accept a third value specifying the change between values.
 range(start, stop, step) - the integers between start (inclusive)
and stop (exclusive) by step
 Example:
for x in range(5, 0, -1):
print x
print "Blastoff!"
Output:
5
4
3
2
1
Blastoff!

10. Grouping Indentation
In Python:
for i in range(20):
if i%3 == 0:
print (i)
if i%5 == 0:
print ("Bingo!”)
print ("---”)
0
Bingo!
---
---
---
3
---
---
---
6
---
---
---
9
---
---
---
12
---
---
---
15
Bingo!
---
---
---
18
---
---

11. while
 while loop: Executes a group of statements as long as a
condition is True.
 good for indefinite loops (repeat an unknown number of times)
 Syntax:
while condition:
statements
 Example:
number = 1
while number < 200:
print number,
number = number * 2
 Output:
1 2 4 8 16 32 64 128

12. if
if statement: Executes a group of
statements only if a certain condition
is true. Otherwise, the statements are
skipped.
Syntax:
if condition:
statements
Example:
gpa = 3.4
if gpa > 2.0:
print "Your application is accepted."

13. if/else
 if/else statement: Executes one block of statements if a certain
condition is True, and a second block of statements if it is False.
 Syntax:
if condition:
statements
else:
statements
 Example:
gpa = 1.4
if gpa > 2.0:
print "Welcome to Mars University!"
else:
print "Your application is denied."
 Multiple conditions can be chained with elif ("else if"):
if condition:
statements
elif condition:
statements
else:
statements

14. Logic
 Many logical expressions use relational operators:
 Logical expressions can be combined with logical operators:
Operator Example Result
and 9 != 6 and 2 < 3 True
or 2 == 3 or -1 < 5 True
not not 7 > 0 False
Operator Meaning Example Result
== equals 1 + 1 == 2 True
!= does not equal 3.2 != 2.5 True
< less than 10 < 5 False
> greater than 10 > 5 True
<= less than or equal to 126 <= 100 False
>= greater than or equal to 5.0 >= 5.0 True

15. import random
print ("Let's calculate Pin")
c=0
maxx=1000
for l in range(1,maxx):
# print ("We're generating point %d" % (l))
x = random.uniform(0,1)
y = random.uniform(0,1)
# print ("(" + str(x) + "," + str(y) + ")",end="n")
r = x*x + y*y
# print ("r = " + str(r))
if r < 1:
# print ("In the circle",end="n")
c+=1
p = float(c)*4/float(l)
print ("Pi estimate after " + str(maxx) + " iterations = " + str(p) + "n")

16. PI-thon.py
Introduction
Buffon's Needle is one of the oldest problems
in the field of geometrical probability. It
was first stated in 1777. It involves
dropping a needle on a lined sheet of paper
and determining the probability of the
needle crossing one of the lines on the page.
The remarkable result is that the probability
is directly related to the value of pi.
https://www.youtube.com/watch?v=Vws1jvM
bs64&feature=youtu.be

17. Python Videos
http://python.org/
- documentation, tutorials, beginners guide, core
distribution, ...
Books include:
 Learning Python by Mark Lutz
 Python Essential Reference by David Beazley
 Python Cookbook, ed. by Martelli, Ravenscroft and
Ascher

18. Overview
What is Python ?
Why Python 4 Bioinformatics ?
How to Python
IDE: Eclipse & PyDev / Athena
Code Sharing: Git(hub)
Strings

19.  string: A sequence of text characters in a program.
 Strings start and end with quotation mark " or apostrophe ' characters.
 Examples:
"hello"
"This is a string"
"This, too, is a string. It can be very long!"
 A string may not span across multiple lines or contain a " character.
"This is not
a legal String."
"This is not a "legal" String either."
 A string can represent characters by preceding them with a backslash.
 t tab character
 n new line character
 " quotation mark character
 backslash character
 Example: "HellottherenHow are you?"
Strings

20. Indexes
 Characters in a string are numbered with indexes starting at 0:
 Example:
name = "P. Diddy"
 Accessing an individual character of a string:
variableName [ index ]
 Example:
print name, "starts with", name[0]
Output:
P. Diddy starts with P
index 0 1 2 3 4 5 6 7
character P . D i d d y

21. Strings
• "hello"+"world" "helloworld" # concatenation
• "hello"*3 "hellohellohello" # repetition
• "hello"[0] "h" # indexing
• "hello"[-1] "o" # (from end)
• "hello"[1:4] "ell" # slicing
• len("hello") 5 # size
• "hello" < "jello" 1 # comparison
• "e" in "hello" 1 # search
• "escapes: n etc, 033 etc, if etc"
• 'single quotes' """triple quotes""" r"raw strings”
• "hello"[1:4:-1] "olleh” #
reversed

22. String properties
 len(string) - number of characters in a string
(including spaces)
 str.lower(string) - lowercase version of a string
 str.upper(string) - uppercase version of a string
 Example:
name = "Martin Douglas Stepp"
length = len(name)
big_name = str.upper(name)
print big_name, "has", length,
"characters"
Output:
MARTIN DOUGLAS STEPP has 20 characters
a.replace

23. Text processing
 text processing: Examining, editing, formatting
text.
 often uses loops that examine the characters of a string
one by one
 A for loop can examine each character in a string
in sequence.
 Example:
for c in "booyah":
print c
Output:
b
o
o
y
a
h

24. Strings and numbers
 ord(text) - converts a string into a number.
 Example: ord("a") is 97, ord("b") is 98, ...
 Characters map to numbers using standardized mappings such
as ASCII and Unicode.
 chr(number) - converts a number into a string.
 Example: chr(99) is "c"
 Exercise: Write a program that performs a rotation cypher.
 e.g. "Attack" when rotated by 1 becomes "buubdl"

25. Lists
• Flexible arrays, not Lisp-like linked
lists
• a = [99, "bottles of beer", ["on", "the",
"wall"]]
• Same operators as for strings
• a+b, a*3, a[0], a[-1], a[1:], len(a)
• Item and slice assignment
• a[0] = 98
• a[1:2] = ["bottles", "of", "beer"]
-> [98, "bottles", "of", "beer", ["on", "the", "wall"]]
• del a[-1] # -> [98, "bottles", "of", "beer"]

26. More List Operations
>>> a = range(5) # [0,1,2,3,4]
>>> a.append(5) # [0,1,2,3,4,5]
>>> a.pop() # [0,1,2,3,4]
>>> a.insert(0, 42) # [42,0,1,2,3,4]
>>> a.pop(0) # [0,1,2,3,4]
>>> a.reverse() # [4,3,2,1,0]
>>> a.sort() # [0,1,2,3,4]

27. Dictionaries
• Hash tables, "associative arrays"
• d = {"duck": "eend", "water": "water"}
• Lookup:
• d["duck"] -> "eend"
• d["back"] # raises KeyError exception
• Delete, insert, overwrite:
• del d["water"] # {"duck": "eend", "back": "rug"}
• d["back"] = "rug" # {"duck": "eend", "back":
"rug"}
• d["duck"] = "duik" # {"duck": "duik", "back":
"rug"}

28. More Dictionary Ops
• Keys, values, items:
• d.keys() -> ["duck", "back"]
• d.values() -> ["duik", "rug"]
• d.items() -> [("duck","duik"),
("back","rug")]
• Presence check:
• d.has_key("duck") -> 1; d.has_key("spam") -
> 0
• Values of any type; keys almost any
• {"name":"Guido", "age":43,
("hello","world"):1,
42:"yes", "flag": ["red","white","blue"]}

29. Dictionary Details
• Keys must be immutable:
– numbers, strings, tuples of immutables
• these cannot be changed after creation
– reason is hashing (fast lookup technique)
– not lists or other dictionaries
• these types of objects can be changed "in
place"
– no restrictions on values
• Keys will be listed in arbitrary order
– again, because of hashing

30. Find the answer in ultimate-sequence.txt
>ultimate-sequence
ACTCGTTATGATATTTTTTTTGAACGTGAAAATACT
TTTCGTGCTATGGAAGGACTCGTTATCGTGAAGT
TGAACGTTCTGAATGTATGCCTCTTGAAATGGA
AAATACTCATTGTTTATCTGAAATTTGAATGGGA
ATTTTATCTACAATGTTTTATTCTTACAGAACAT
TAAATTGTGTTATGTTTCATTTCACATTTTAGTA
GTTTTTTCAGTGAAAGCTTGAAAACCACCAAGA
AGAAAAGCTGGTATGCGTAGCTATGTATATATA
AAATTAGATTTTCCACAAAAAATGATCTGATAA
ACCTTCTCTGTTGGCTCCAAGTATAAGTACGAAA
AGAAATACGTTCCCAAGAATTAGCTTCATGAGT
AAGAAGAAAAGCTGGTATGCGTAGCTATGTATA
TATAAAATTAGATTTTCCACAAAAAATGATCTG
ATAA
Oefening

31. AA1 =
{'UUU':'F','UUC':'F','UUA':'L','UUG':'L','UCU':'S','
UCC':'S','UCA':'S','UCG':'S','UAU':'Y','UAC':'Y','UA
A':'*','UAG':'*','UGU':'C','UGC':'C','UGA':'*','UGG':
'W','CUU':'L','CUC':'L','CUA':'L','CUG':'L','CCU':'P',
'CCC':'P','CCA':'P','CCG':'P','CAU':'H','CAC':'H','CA
A':'Q','CAG':'Q','CGU':'R','CGC':'R','CGA':'R','CGG'
:'R','AUU':'I','AUC':'I','AUA':'I','AUG':'M','ACU':'T','
ACC':'T','ACA':'T','ACG':'T','AAU':'N','AAC':'N','AAA'
:'K','AAG':'K','AGU':'S','AGC':'S','AGA':'R','AGG':'R',
'GUU':'V','GUC':'V','GUA':'V','GUG':'V','GCU':'A','G
CC':'A','GCA':'A','GCG':'A','GAU':'D','GAC':'D','GA
A':'E','GAG':'E','GGU':'G','GGC':'G','GGA':'G','GGG
':'G' }
Dictionary