python course in bioinformatics - university of california...

OutlineGeneral Introduction

Basic Types in PythonProgramming

Exercises

Python course in Bioinformatics

Xiaohui Xie

March 31, 2009

Xiaohui Xie Python course in Bioinformatics



Exercises

General Introduction

Basic Types in Python

Programming

Exercises




Exercises

Why Python?

I Scripting language, raplid applications

I Minimalistic syntax

I Powerful

I Flexiablel data structure

I Widely used in Bioinformatics, and many other domains




Exercises

Where to get Python and learn more?

I Main source of information: http://docs.python.org/

I Tutorial: http://docs.python.org/tutorial/index.html

I Biopython: http://biopython.org/wiki/Main Page


http://docs.python.org/

http://docs.python.org/tutorial/index.html

http://biopython.org/wiki/Main_Page



Exercises

Invoking Python

I To start: type python in command lineI It will look like

Python 2.5.2 (r252:60911, Mar 25 2009, 00:12:33)

[GCC 4.1.2 (Gentoo 4.1.2 p1.0.2)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

>>>

I You can now type commands in the line denoted by >>>

I To leave: type end-of-file character ctrl-D on Unix, ctrl-zon Windows

I This is called interactive mode




Exercises

Appetizer Example

I Task: Print all numbers in a given fileI File: numbers.txt

2.1

3.2

4.3

I Code: print.py

# Note: the code lines begin in the first column of the file. In

# Python code indentation *is* syntactically relevant. Thus, the

# hash # (which is a comment symbol, everything past a hash is

# ignored on current line) marks the first column of the code

data = open("numbers.txt", "r")

for d in data:

print d

data.close()




Exercises

Appetizer Example cont’d

I Task: Print the sum of all the data in the fileI Code: sum.py

data = open("numbers.txt", "r")

s = 0

for d in data:

s = s + float(d)

print s

data.close()




Exercises

Interative Mode

I prompt >>> allows to enter command

I command is ended by newline

I variables need not be initialized or declared

I a colon “:” opens a block

I ... prompt denotes that block is expected

I no prompt means python output

I a block is indented

I by ending indentation, block is ended




Exercises

Differences to Java or C

I can be used interatively. This makes it much easier to testprograms and to debug

I no declaration of variables

I no brackets denote block, just indentation (Emacs supportsthe style)

I a comment begins with a “#”. Everything after that isignored.




Exercises

Numbers

I Example

>>> 2+2

4

>>> # This is a comment

... 2+2

4

>>> 2+2 # and a comment on the same line as code

4

>>> (50-5*6)/4

5

>>> # Integer division returns the floor:

... 7/3

2

>>> 7/-3

-3




Exercises

Numbers cont’d

I Example

>>> width = 20

>>> height = 5*9

>>> width * height

900

>>> # Variables must be defined (assigned a value) before they can be

>>> # used, or an error will occur:

>>> # try to access an undefined variable

... n

Traceback (most recent call last):

File "<stdin>", line 1, in <module>

NameError: name ’n’ is not defined




Exercises

Strings

I Strings can be enclosed in single quotes or double quotesI Example

>>> ’spam eggs’

’spam eggs’

>>> ’doesn\’t’

"doesn’t"

>>> "doesn’t"

"doesn’t"

>>> ’"Yes," he said.’

’"Yes," he said.’

>>> "\"Yes,\" he said."

’"Yes," he said.’

>>> ’"Isn\’t," she said.’

’"Isn\’t," she said.’




Exercises

Strings cont’d

I Strings can be surrounded in a pair of matching triple-quotes:""" or ’’’. End of lines do not need to be escaped whenusing triple-quotes, but they will be included in the string.

I Example

print """

Usage: thingy [OPTIONS]

-h Display this usage message

-H hostname Hostname to connect to

"""




Exercises

Strings cont’d

I Strings can be concatenated (glued together) with the +operator, and repeated with *:

I Example

>>> word = ’Help’ + ’A’

>>> word

’HelpA’

>>> ’<’ + word*5 + ’>’

’<HelpAHelpAHelpAHelpAHelpA>’

>>> ’str’ ’ing’ # <- This is ok

’string’

>>> ’str’.strip() + ’ing’ # <- This is ok

’string’




Exercises

Strings cont’d

I Strings can be subscripted (indexed); like in C, the firstcharacter of a string has subscript (index) 0.

I There is no separate character type; a character is simply astring of size one.

I Substrings can be specified with the slice notation: twoindices separated by a colon.

I Example

>>> word = ’Help’ + ’A’

>>> word[4]

’A’

>>> word[0:2]

’He’

>>> word[:2] # The first two characters

’He’

>>> word[2:] # Everything except the first two characters

’lpA’




Exercises

Strings cont’d

I Unlike a C string, Python strings cannot be changed.Assigning to an indexed position in the string results in anerror:

I Example

>>> word[0] = ’x’

Traceback (most recent call last):

File "<stdin>", line 1, in ?

TypeError: object doesn’t support item assignment

>>> ’x’ + word[1:]

’xelpA’

>>> ’Splat’ + word[4]

’SplatA’




Exercises

Strings cont’d

I Example

>>> from string import *

>>> dna = ’gcatgacgttattacgactctg’

>>> len(dna)

22

>>> ’n’ in dna

False

>>> count(dna,’a’)

5

>>> replace(dna, ’a’, ’A’)

’gcAtgAcgttAttAcgActctg’

I Exercise: Calculate GC percent of dna




Exercises

Strings cont’d

I Solution: Calculate GC percent

>>> gc = (count(dna, ’c’) + count(dna, ’g’)) / float(len(dna)) * 100

>>> "%.2f" % gc

’64.08’




Exercises

Strings cont’d

I Exercise: Calculate the complement of DNA

A - T

C - G




Exercises

Lists

I A list of comma-separated values (items) between squarebrackets.

I List items need not all have the same type (compund datatypes)

>>> a = [’spam’, ’eggs’, 100, 1234]

>> a[0]

’spam’

>>> a[3]

1234

>>> a[-2]

100

>>> a[1:-1]

[’eggs’, 100]

>>> a[:2] + [’bacon’, 2*2]

[’spam’, ’eggs’, ’bacon’, 4]

>>> 3*a[:3] + [’Boo!’]

[’spam’, ’eggs’, 100, ’spam’, ’eggs’, 100, ’spam’, ’eggs’, 100, ’Boo!’]




Exercises

Lists cont’d

I Unlike strings, which are immutable, it is possible to changeindividual elements of a list

I Assignment to slices is also possible, and this can even changethe size of the list or clear it entirely

I Example

>>> a

[’spam’, ’eggs’, 100, 1234]

>>> a[2] = a[2] + 23

>>> a[0:2] = [1, 12] # Replace some items:

>>> a[0:2] = [] # Remove some:

>>> a

[123, 1234]

>>> a[1:1] = [’bletch’, ’xyzzy’] # Insert some:

>>> a

[123, ’bletch’, ’xyzzy’, 1234]




Exercises

Lists cont’d

I Functions returning a list

>>> range(3)

[0, 1, 2]

>>> range(10,20,2)

[10, 12, 14, 16, 18]

>>> range(5,2,-1)

[5, 4, 3]

>>> aas = "ALA TYR TRP SER GLY".split()

>>> aas

[’ALA’, ’TYR’, ’TRP’, ’SER’, ’GLY’]

>>> " ".join(aas)

’ALA TYR TRP SER GLY’

>>> l = list(’atgatgcgcccacgtacga’)

[’a’, ’t’, ’g’, ’a’, ’t’, ’g’, ’c’, ’g’, ’c’, ’c’, ’c’, ’a’,

’c’, ’g’, ’t’, ’a’, ’c’, ’g’, ’a’]




Exercises

Dictionaries

I A dictionary is an unordered set of key: value pairs, with therequirement that the keys are unique

I A pair of braces creates an empty dictionary: .I Placing a comma-separated list of key:value pairs within the

braces adds initial key:value pairs to the dictionaryI The main operations on a dictionary are storing a value with

some key and extracting the value given the keyI Example

>>> tel = {’jack’: 4098, ’sape’: 4139}

>>> tel[’guido’] = 4127

>>> tel

{’sape’: 4139, ’guido’: 4127, ’jack’: 4098}

>>> tel[’jack’]

4098




Exercises

Dictionaries cont’d

I Example

>>> tel = {’jack’: 4098, ’sape’: 4139, ’guido’ = 4127}

>>> del tel[’sape’]

>>> tel[’irv’] = 4127

>>> tel

{’guido’: 4127, ’irv’: 4127, ’jack’: 4098}

>>> tel.keys()

[’guido’, ’irv’, ’jack’]

>>> ’guido’ in tel

True




Exercises

Programming

I Example

a, b = 3, 4

if a > b:

print a + b

else:

print a - b




Exercises

Programming cont’d

I Example

>>> # Fibonacci series:

... # the sum of two elements defines the next

... a, b = 0, 1

>>> while b < 10:

... print b

... a, b = b, a+b

...

1

1

2

3

5

8




Exercises

Programming features

I multiple assignment: rhs evaluated before anything on theleft, and (in rhs) from left to right

I while loop executes as long as condition is True (non-zero,not the empty string, not None)

I block indentation must be the same for each line of block

I need empty line in interactive mode to indicate end of block(not required in edited code)

I use of print




Exercises

Printing

I Example

>>> i = 256*256

>>> print ’The value of i is’, i

The value of i is 65536




Exercises

Flow control

I Example

x = 35

if x < 0:

x = 0

print ’Negative changed to zero’

elif x == 0:

print ’Zero’

elif x == 1:

print ’Single’

else:

print ’More’




Exercises

Iteration

I Python for iterates over sequence (string, list, generatedsequence)

I Example

a = [’cat’, ’window’, ’defenestrate’]

for x in a:

print x, len(x)




Exercises

Definiting functions

I Example

def fib(n): # write Fibonacci series up to n

"""Print a Fibonacci series up to n."""

a, b = 0, 1

while b < n:

print b,

a, b = b, a+b

# Now call the function we just defined:

fib(2000)

# will return:

# 1 1 2 3 5 8 13 21 34 55 89 144 233 377 610 987 1597




Exercises

Reverse Complement of DNA

I Excercise: Find the reverse complement of a DNA sequenceI Example

5’ - ACCGGTTAATT 3’ : forward strand

3’ - TGGCCAATTAA 5’ : reverse strand

So the reverse complement of ACCGGTTAATT is AATTAACCGGA




Exercises

Reverse Complement of DNA

I Solution: Find the reverse complement of a DNA sequence

from string import *

def revcomp(dna):

""" reverse complement of a DNA sequence """

comp = dna.translate(maketrans("AGCTagct", "TCGAtcga"))

lcomp = list(comp)

lcomp.reverse()

return join(lcomp, "")




Exercises

Translate a DNA sequence

I Excercise: Translate a DNA sequence to an amino acidsequence

I Genetic code

standard = { ’ttt’: ’F’, ’tct’: ’S’, ’tat’: ’Y’, ’tgt’: ’C’,

’ttc’: ’F’, ’tcc’: ’S’, ’tac’: ’Y’, ’tgc’: ’C’,

’tta’: ’L’, ’tca’: ’S’, ’taa’: ’*’ , ’tca’: ’*’,

’ttg’: ’L’, ’tcg’: ’S’, ’tag’: ’*’, ’tcg’: ’W’,

’ctt’: ’L’, ’cct’: ’P’, ’cat’: ’H’, ’cgt’: ’R’,

’ctc’: ’L’, ’ccc’: ’P’, ’cac’: ’H’, ’cgc’: ’R’,

’cta’: ’L’, ’cca’: ’P’, ’caa’: ’Q’, ’cga’: ’R’,

’ctg’: ’L’, ’ccg’: ’P’, ’cag’: ’Q’, ’cgg’: ’R’,

’att’: ’I’, ’act’: ’T’, ’aat’: ’N’, ’agt’: ’S’,

’atc’: ’I’, ’acc’: ’T’, ’aac’: ’N’, ’agc’: ’S’,

’ata’: ’I’, ’aca’: ’T’, ’aaa’: ’K’, ’aga’: ’R’,

’atg’: ’M’, ’acg’: ’T’, ’aag’: ’K’, ’agg’: ’R’,

’gtt’: ’V’, ’gct’: ’A’, ’gat’: ’D’, ’ggt’: ’G’,

’gtc’: ’V’, ’gcc’: ’A’, ’gac’: ’D’, ’ggc’: ’G’,

’gta’: ’V’, ’gca’: ’A’, ’gaa’: ’E’, ’gga’: ’G’,

’gtg’: ’V’, ’gcg’: ’A’, ’gag’: ’E’, ’ggg’: ’G’ }


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