Introduction to Python

The metabolic modelling we will be using, ScrumPy, is written in Python. Python is a high-level, object-oriented, interpreted programming language, it has a large standard library, and supports multiple programming paradigms. It is also syntactically clear and easy to learn. This is a very brief introduction to some of the basic features of the language, for a more complete introduction to the topic, see Lutz & Ascher, "Learning Python" O'Reilly Media inc. (Edition 2 or greater). A good source of Python documentation can be found here.

Getting started

We will be using Python from the ScrumPy environment. To start a new ScrumPy session open a terminal and type "ScrumPy":

user@machine:~$ ScrumPy &

which will launch the ScrumPy window.

Data types

Numbers

The numerical types we will be dealing with are integers, int, and floating-point numbers float. Integers are written as a sequence of digits. Floats are written as digits with a decimal point in the sequence, and an optional exponent (e or E).

   1 >>> n_int = 135
   2 >>> n_int
   3 135
   4 >>> n_float = 10e-10
   5 >>> n_float
   6 1.0000e-9

The type of a given data object can be checked using the built-in function type().

>>> type(n_int)
<type 'int'>
>>>type(n_float)
<type 'float'>

Floats and integers can be interconverted using the constructors int() or float().

>>> n_int2float=float(n_int)
>>> n_int2float
135.0
>>> type(n_int2float)
<type 'float'>   #n_int is still an integer

The common matematical operators (+,-,/,*) work as expected, note that x**y means x^y.

Boolean

Booleans are a subtype of integers. A boolean type is either True or False, and can be very useful when writing conditional statements, i.e. if something is True, do something. Also, the integer 0 is False.

>>> val=True
>>> if val:
        print 'val is true'

val is true

>>> val=False
>>> if val:
        print 'val is true'

>>> 

Strings

Strings are collections of characters. Characters in a string can be accessed by indexing, and membership of a subset of characters in a string can be evaluated.

>>> s_1 = 'another string'   #create string
>>> s_2 = s_1[:7]            #create new string of characters 0 to 7 in s_1
>>> s_2
'another'
>>> if s_2 in s_1:          #check for membership of s_2 in s_1
        print 'true'

true
>>> type(s_1)
<type 'str'>
>>> str(n_int)
'135'

Lists (and tuples)

Lists and tuples are collections of objects. The main difference between the two is that tuples are immutable - once a tuple is created it cannot be changed, whereas lists can. For these excercises we will only use lists. An empty list can be created by assigning a pair of closed square brackets to a variable.

>>> empyt_list=[]

Dictionaries

Modules

Objects

Loops and conditionals