Python Programming for Biology: Bioinformatics and Beyond

Method

Description

Example

seq.append(val)

Adds a single item to the end of

a list.

x = [True, False]

x.append(None)

# [True, False,

None]

seq.extend(vals)

Adds one or more items from a

collection onto the end of a list.

x = [1,2]

y = [3,4]

x.extend(y)

# x is [1, 2, 3, 4]

seq.count(val)

Counts the number of

occurrences of a given item.

x = [7,9,2,7,1]

x.count(7) # 2

seq.index(val, start,

end)

Determines the index of the

first occurrence of an item,

within an optional index range.

x = [7,9,2,7,1]

x.index(7) # 0

x.index(7,1) # 3

seq.insert(index,

val)

Inserts an item at a given

positional index within a list,

increasing the length of the list

by one.

x = [1,2,2,1]

x.insert(2,4)

# [1, 2, 4, 2, 1]

seq.pop(index)

Removes and passes back an

item from a list, reducing the

length of the list by one.

Defaults to remove the last

item, otherwise an index may

be specified.

x =

['a','b','c','d']

x.pop() # 'd'; x now

['a', 'b', 'c']

x.pop(1) # 'b'; x

now ['a', 'c']

seq.remove(val)

Removes the first occurrence of

an item from a list.

x = [1,2,3,2,1]

x.remove(2)

# [ 1, 3, 2, 1]

seq.reverse()

Reverses the order of items of

the list. Does not generate a

x =

['a','b','c','d']

---

new list.

x.reverse()

# ['d', 'c', 'b',

'a']

seq.sort(comparator,

key, reverse)

Above for Python 2

seq.sort(key,

reverse)

Above for Python 3

Sorts the items of a list, using

optional comparison function

(in Python 2) and key attribute.

Option to sort in reverse order.

x = [7,9,2,7,1]

x.sort()

# [1, 2, 7, 7, 9]

x.sort(reverse=True)

# [9, 7, 7, 2, 1]

Set operations

The  set  and  the  immutable  equivalent  frozenset  are  Python’s  standard  unordered  non-

repeating collection data types. The following table lists common operations and methods

for  sets  (and  where  appropriate  frozen  sets).  Sets  may  be  specified  with  the  inbuilt  set()

function,  operating  on  another  collection,  e.g.  set([a,b,c])  and  also  (from  Python  2.7

onwards) by using the curly brace notation {a,b,c}, which differs from dictionaries due to

the absence of colons. Using set() with no arguments or on an empty collection creates an

empty  set,  but  {}  does  not;  it  is  an  empty  dictionary.  For  the  descriptions  below  we  list

methods of sets in the form s.method(args) and also any equivalents that can be performed

with a symbolic operator syntax. For example, set3 = set1.union(set2) is equivalent to set3

= set1 | set2.