Python Programming for Biology: Bioinformatics and Beyond

Method

Description

Example

s.capitalize()

Generates a copy of a

string where the first

character is capitalised, if

it is a lower-case letter.

'abc'.capitalize() #

'Abc'

'Abc'.capitalize() #

'Abc'

'1abc'.capitalize()

#'1abc'

s.count(substr,

start, end)

Counts the number of

occurrences (without

overlap) of a substring

within a larger string.

Optional index range

arguments.

text = 'Bananarama'

text.count('a') # 5

text.count('q') # 0

text.count('an') # 2

text.count('ana') # 1

s.endswith(substr,

start, end)

Determines whether a

string ends with a given

substring. Optional

position range

'xyz'.endswith('z') #

True

'xyz'.endswith('y') #

False

---

arguments.

'xyz'.endswith('yz')#

True

'xyz'.endswith('y',0,2)

# True

s.find(substr,

start, end)

Gives the starting index

of the first occurrence of

a substring within a

larger string, or −1 if

none is found. Optional

index range arguments.

text = 'Bananarama'

text.find('r') # 6

text.find('a') # 1

text.find('q') # -1

text.find('am') # 7

s.format(*args, **kwd)

Generates a specially

formatted version of a

string.

[See formatting in

Appendix 4

below]

s.index(substr,

start, end)

Gives the starting index

of the first occurrence of

a substring within a

larger string. Creates a

ValueError if none is

found. Optional index

range arguments.

text = 'Bananarama'

text.index('a') # 1

text.index('am') # 7

text.index('q') #

Fails!

s.isalnum()

Determines whether a

string contains only

alphanumeric characters.

Gives True if so, and

False otherwise.

'ab12'.isalnum() # True

'ab/12'.isalnum() #

False

s.isalpha()

Determines whether a

string contains only

letters of the alphabet.

'abc'.isalpha() # True

'abc?'.isalpha() #

False

s.isdigit()

Determines whether a

string contains only

numeric digit characters.

Gives True if so, and

False otherwise.

'10'.isdigit() # True

'1.0'.isdigit() # False

s.islower()

Determines whether a

string contains letters that

are all lower case. Gives

True if so, and False

otherwise.

'abc'.islower() # True

'Abc'.islower() # False

'ab@#12'.islower() #

True

'@#12'.islower() #

---

False

s.isspace()

Determines whether a

string contains only

whitespace characters.

Gives True if so, and

False otherwise.

' '.isspace() # True

'a'.isspace() # False

' a'.isspace() # False

'\t\n '.isspace() #

True

s.isupper()

Determines whether a

string contains letters that

are all upper case. Gives

True if so, and False

otherwise.

'ABC'.isupper () # True

'Abc'.isupper () #

False

'AB@#12'.isupper() #

True

'@#12'.isupper() #

False

s.join(iterable)

Uses one string to join

the items (which must

also be strings) that come

from a sequence

collection, or other

iterable object, to form a

new string.

x = ['G','C','A','T']

sep = ','

sep.join(x) # 'G,C,A,T'

'; '.join(x) # 'G; C;

A; T'

'/'.join(('AC','DC'))

# 'AC/DC'

s.lower()

Generates a copy of a

string where any upper-

case characters are

converted to lower case.

'Ala258'.lower() #

'ala258'

'ALA258'.lower() #

'ala258'

s.lstrip(chars)

Generates a copy of a

string where specified

characters at the start

(left) are removed.

Optional string argument

to specify which

characters to consider,

otherwise it is leading

whitespace which is

removed.

' X Y '.lstrip() # 'X

Y '

s.replace(old, new,

maxNum)

Generates one string

from another by

rna = 'AUGCAUAGCA'

dna =

---

replacing all occurrences

of one substring with

another substring.

Optional maximum

number of replacements.

rna.replace('U','T')

Result is 'ATGCATAGCA'.

s.rfind(substr,

start, end)

Like find(), but gives the

starting index of the last

occurrence of a substring

within a larger string, or

−1 if none is found.

text = 'Bananarama'

text.rfind('r') # 6

text.rfind('a') # 9

text.rfind('q') # -1

s.rindex(substr,

start,

end)

Like index(), but gives

the starting index of the

last occurrence of a

substring within a larger

string. Creates a

ValueError if none is

found.

text = 'Bananarama'

text.rindex('a') # 9

text.rindex('am') # 7

text.rindex('q') #

Fails!

s.rstrip(chars)

Generates a copy of a

string where specified

characters at the end

(right) are removed.

Optional string argument

to specify which

characters to consider,

otherwise it is trailing

whitespace which is

removed.

' X Y '.rstrip() # '

X Y'

s.split(sep, maxNum)

Generates a list of strings

by splitting a string into

parts where a substring is

found. If substring is not

specified then split on

whitespace.

t = 'G, C, A, T'

t.split(', ')

# ['G','C','A','T']

t.split(':')

# ['G, C, A, T']

s.splitlines(keepends)

Generates a list of strings

by splitting a string into

parts where newline

(‘\n’, ‘\r’, ‘\r\n’)

characters are found.

text = 'AC\nDC'

text.splitlines() #

['AC', 'DC']

s.startswith(prefix,

Determines whether a

string starts with a given

'xyz'.startswith('x') #

---

start,

end)

substring. Optional

position range

arguments.

True

'xyz'.startswith('y') #

False

'xyz'.startswith('xy')

# True

'xyz'.startswith('y',1)

# True

s.strip(chars)

Generates a copy of a

string where specified

characters at either end

are removed. Optional

string argument to

specify which characters

to consider, otherwise it

is whitespace which is

removed.

' X Y '.strip() # 'X

Y'

s.title()

Generates a copy of a

string where the first

character of each group

of letters is capitalised.

' hi joe '.title() # '

Hi Joe '

s.translate(table,

delChars)

Generates one string

from another by using a

256-character translation

table to map characters,

and optionally also delete

characters.

from string import

maketrans

table =

maketrans('U','T') # v2

rna = 'AUGCAUAGCA'

dna =

rna.translate(table)

Result is 'ATGCATAGCA'.

In Python 3 second line

instead is:

table =

str.maketrans('U','T')

s.upper()

Generates a copy of a

string where any lower-

case characters are

converted to upper case.

'ala258'.upper() #

'ALA258'

'Ala258'.upper() #

'ALA258'

s.zfill(width)

Fill a string with zero

characters ‘0’, up to a

given total width.

'7'.zfill(3) # '007'

'7'.zfill(1) # '7'

---

List operations

The following table describes some of the operations and inbuilt methods for Python lists

and related sequence containers, which are generally represented as seq. It should be noted

that  a  collection  object  (set,  tuple,  other  list  …)  can  be  converted  to  a  list  using

list(collection) and that list() generates an empty list, just like[].

Operation

Description

Example

len(seq)

Determines the number of items in the

list; its length.

letters =

['G','C','A','T']

len(letters) # 4

seq[i] =

obj

Sets the item at a given index position in

a list.

letters =

['G','C','A','T']

letters[3] = 'U'

# ['G','C','A','U']

seq[i:j] =

vals

Sets a number of items covering a range

of positional indices; from a starting

positional index and up to but not

including a second index.

nums = [1,2,3,4,5,6]

nums[2:] = [3,2,1]

# [1, 2, 3, 2, 1]

vals =

seq[i:j]

Extracts number of items covering a

range of positional indices as a new list;

from a starting positional index and up

to but not including a second index.

nums = [1,2,3,4,5,6]

new1 = nums[3:]

# [4,5,6]

new2 = nums[:] # Copy

all

del seq[i:j]

Deletes an item or range of items from a

list of specified indices.

nums = [1,2,3,4,5,6]

del nums[1:5]

# [1, 6]

seq[i:j:k]

= vals

Sets a number of items covering a range

of positional indices with a given step.

myList =

[0,0,0,0,0,0]

myList[1::2] =

[1,1,1]

# [0, 1, 0, 1, 0, 1]

del

seq[i:j:k]

Deletes a number of items covering a

range of positional indices with a given

step.

letters =

['A','B','C','D','E']

del letters[::2]

---

# ['B', 'D']