Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

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This function is present in

Python 2 and from Python

2.6 is the same as the

function in Python 3 by using

from __future__ import

print_function. It replaces the

print statement which is in

Python 2 but not in Python 3.

Prints a textual representation

of one or more Python

objects to the screen or file.

x = 'Some data'

print(x)


print(x, file=fileObj)

#Python 3

print(1,2,3)

Result is 1 2 3.

print(1, 2, 3, sep=';',

end='*\n')

Result is 1;2;3*.

property(getFunc,



setFunc, delFunc,

docStr)

Allows attribute-style dot

notation access

(classObj.attrName) for

getter and setter functions in

‘new-style’ class definitions

(which inherit from object).

class DemoObj(object):

def __init__(self):

self._x = None

def getX(self):

return self._x

def setX(self,

value):



This means that the code

looks cleaner and allows

extra functionality, for

example, validation in the

setter function. Optionally

there is a third argument

which is a function for

attribute deletion, and a

fourth argument, which is a

document string.

self._x = value

x = property(getX,

setX)

d = DemoObj()



d.x = 55 # same as

d.setX(55)

print(d.x) # same as

d.getX()


Result is 55.

range(end)

or

range(start, end,



step)

Gives a range of integers

from a start up to (but not

including) an end value with

a regular increment. By

default the range starts at 0

and increments by 1. In

Python 2 range() creates a

list, but in Python 3 becomes

an iterable object, more like

xrange(), and xrange() itself

disappears.

range(7) # [0,1,2,3,4,5,6]

range(3,8) # [3, 4, 5, 6, 7]

range(3,10,2) # [3, 5, 7, 9]

range(5,0,-1) # [5, 4, 3, 2,

1]

In Python 3 the result is not



a list but instead a range

iterable.

raw_input(prompt)

Prompts the user at the

command line for keyboard

input, i.e. so the entered

values can be used in the

program. Not available in

Python 3, use input() instead.

x = raw_input(‘Enter

value:’)

print(“Value is: “, x)

reload(module)

Reloads a Python module,

assuming it was previously

imported. Not available in

Python 3.

import math

math.pi = 3.0

print(math.pi) # 3.0

reload(math)

print(math.pi) #

3.14159265359

repr(obj)

Creates a formal, textual

representation of a Python

object. Similar to str(), but

gives unambiguous (in terms

of identifying the original

object), albeit sometimes less

readable, text.

from numpy import array

a = array([1,2,3])

str(a) # '[1 2 3]'

repr(a) # 'array([1, 2,

3])'


reversed(seq)

Creates an iterator object that

for x in



provides items in the reverse

order, based on an ordered

collection.

reversed(range(7)):

print(x)

round(val, places)

Rounds val to the nearest

whole number or optionally

accepts places, stating how

many decimal places to round

to.

[See Mathematics section



above]

set(vals)

Creates a set from a given

object; an unordered

collection of non-repeating

items.


l = [0,1,2,3,1,2,3,2,1,0,1,3]

x = set(l)

print(x)

Result is set([0, 1, 2, 3]).

setattr(obj, name,

val)


Sets a named attribute of a

specified object with a given

value. This is often an

alternative to the object.attr =

value notation where the

name of the attribute can

vary.

p1 = Molecule()



setattr(p1, ‘name’, ‘c-Myc’)

p1.name = ‘c-Myc’ # Same

sorted(vals,

comparator, key,

reverse)

Creates a new list with items

in sorted order from the items

of a collection or other

iterable object.

list1 = [‘G’,‘C’,‘A’,‘T’]

list2 = sorted(list1)

print(list2)

Result is [‘A’,‘C’,‘G’,‘T’].

str(obj)

Converts a Python object into

an informal textual string

representation. Numeric

values may be rounded for

display.

str(7.500000000001) #

'7.5'

str([5,7,11]) # '[5, 7,



11']

str(type(1)) # "

'int'>"

sum(vals, start)

Adds all the items of a

collection or other iterable

object. For NumPy arrays it

sums along the first axis.

values =

[7,69,31,99,53,16,72]

print(sum(values)) #

347


super(objType,

obj)

When a function is

overridden in a subclass this

allows calling of a superclass

function without mentioning

class C(B):

def f(self, arg):

super(C,

self).f(arg)



the superclass by name. An

optional object (or class) may

be passed in as a second

argument.

# same as doing:

# B.f(self, arg)

tuple(vals)

Creates a Python tuple

collection from a specified

object, which must be

iterable. Can be used on a

tuple to make a copy.

Sometimes used to convert a

list, so that it may be used as

a dictionary key.

l = [‘D’,‘E’,‘R’,‘K’,‘H’]

t = tuple(enumerate(l))

Result is ((0,‘D’), (1,‘E’),

(2,‘R’), (3,‘K’), (4,‘H’)).

type(obj)

Gives an object representing

the type of a specified object.

type(1) #

type(‘a’) #

type(type(1)) #

‘type’>


In Python 3 the result is

etc.

unichr(code)

Gives the Unicode character

string for an integer code

number. Performs the inverse

operation to ord() for

Unicode strings. Not

available in Python 3 since

all strings are Unicode.

alpha = u’\u03b1’

i = ord(alpha)

print(unichr(i+1))

Result is u’\u03b2’; ‘β’.

unicode(obj,



encoding)

Converts a Python object into

a Unicode string

representation in a manner

similar to str(). The optional

second argument allows the

encoding type to be specified,

e.g. when converting plain

text. Not available in Python

3, since all strings are

Unicode.

text1 = unicode(3.141)

x = ‘\xce\xb1-helix’

text2 = unicode(x, ‘utf-8’)

Last result is u’\u03b1-

helix’; ‘α-helix’.

xrange(end)

or

xrange(start, end,



step)

Used for looping through

large ranges of numbers.

Compared to range(),

xrange() doesn’t create a

whole list and thus saves

n = 1000000

y = [x**0.5 for x in

xrange(n)]



memory; instead it creates an

iterable object. Not available

in Python 3 since range()

behaves like xrange().

zip(vals1, vals,

…)

Takes items in sequence from



a number of collections (or

other iterable objects) to

make a list of tuples, where

each tuple contains one item

from each collection. Often

used to group items from lists

which have the same index.

Note the inverse operation is

achieved with zip(*c). In

Python 3 the result is a zip

iterator rather than a list.

a = [1,2,3]

b = [‘x’,‘y’,‘z’]

c = list(zip(a,b))

d = list(zip(*c))

Note: list() conversion not

necessary in Python 2.

Result:


c is [(1,‘x’), (2,‘y’), (3,‘z’)]

d is [(1,2,3), (‘x’,‘y’,‘z’)]





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