Python Programming for Biology: Bioinformatics and Beyond

Inbuilt functions

The  following  lightly  describes  selected,  standard  Python  functions  which  require  no

imports to use. See the standard Python documentation for more technical descriptions and

details of all arguments. Optional arguments are specified in italics.

Function

Description

Example

abs(val)

Generates the absolute value

of a number, i.e. its

magnitude, irrespective of

sign.

numbers = [-3,-2,-1,0,1,2,3]

print([abs(x) for x in

numbers])

Result is [3, 2, 1, 0, 1, 2, 3].

all(vals)

Determines whether all the

items in a collection (or other

iterable) have true values.

all([True, False, True]) #

False

all([1,2,3,4]) # True

---

Gives True if they do and

False otherwise. This does

not work on multi-

dimensional NumPy arrays.

any(vals)

Determines whether any of

the items in a collection (or

other iterable object) have

true values. Gives True if so

and False otherwise. This

does not work on multi-

dimensional NumPy arrays.

any([True, False, True]) #

True

any([False, None, 0.0]) #

False

bin(val)

Creates a string representing

the binary version of a

number; 0 and 1 characters

prefixed with ‘0b’. Available

from Python 2.6 onwards.

x = 341

print(bin(x))

Result is ‘0b101010101’.

bool(val)

Determines whether a value

is logically true or false, i.e.

converts a value into a

Boolean object.

bool(0.0) # False

bool(3.0) # True

bool(‘abc’) # True

callable(obj)

Determines whether an object

is callable, i.e. can be

invoked like a function.

Giving True if so and False

otherwise.

y = 1.47

x = abs # The inbuilt

function

print(callable(y),

callable(x)) # False, True

chr(code)

Gives the ASCII character

string for an integer code

number. Performs the inverse

operation to ord().

i = ord(‘A’)

print(chr(i+1))

Result is ‘B’.

cmp(val1, val2)

Compares two objects and

gives back 1 if the first is

larger, −1 if the second is

larger or 0 if they are equal.

Not available in Python 3.

cmp(1,2) # -1

cmp(2,2) # 0

cmp(2,1) # 1

complex(real,

imag)

Creates a complex number

using separate real and

imaginary components.

x = complex(1,-1.4142)

Result is (1-1.4142j); 1-

1.4142i.

---

dict(vals)

Creates a dictionary from a

specified object, e.g. to copy

another dictionary or to

convert a list of

keyword:value pairs.

x = [(1,1),(2,4),(3,9),(4,16)]

y = dict(x)

Result is {1:1, 2:4, 3:9,

4:16}.

dir(obj)

Gives a list of variable names

that are present within the

current program scope, or if

object is specified the names

associated with that object as

attributes.

print(dir())

print(dir(”))

First line shows imports and

declarations. Second line

shows attributes of string

types.

divmod(val1,

val2)

Divide x by y giving the

integer floor and remainder

as separate values.

[See Mathematics section]

enumerate(vals,

start)

Generates sequential pairs of

(number, item) from a

collection or other iterable

object, e.g. extracting objects

and their indices from a list.

Creates an iterator object.

Takes a start number as a

second argument.

letters = ‘GCAT’

enum =

list(enumerate(letters))

Result is [(0,‘G’), (1,‘C’),

(2,‘A’), (3,‘T’)].

eval(exprn, locals,

globals)

Evaluates a string as an

expression in Python syntax,

i.e. to allow the dynamic

generation of expressions.

Allows optional dictionary

arguments to specify global

and local scope variable

names.

text = ‘x*7+5*y’

x = 4.7

y = 8.1

eval(text)

Result is 73.4.

execfile(fileName,