Python Programming for Biology: Bioinformatics and Beyond

Getting started

Firstly,  before  using  Python  it  must  of  course  be  installed  on  your  computer.  For

Macintosh and Linux users Python is generally installed as standard, though you may wish

to  upgrade  if  the  version  is  before  Python  2.6.  For  Windows  users  Python  is  a  simple

double-click install, using the appropriate ‘MSI’ installer file. Windows, Macintosh, Linux

and  UNIX  downloads  are  all  available  from

http://www.python.org

.  However,  for  most

flavours  of  Linux  it  is  easiest  to  install  or  upgrade  Python  via  the  system’s  package

manager.  Later,  in  this  book  we  will  require  that  some  extra  Python  modules  are  also

installed, such as Numeric Python and Scientific Python packages. Because the websites

for these may change in the future we list the up-to-date download locations for all extra

packages

on

the

Cambridge

University

Press

website:

http://www.cambridge.org/pythonforbiology

.

There are two basic ways of running Python. The commands can be read and run from

a file as a script. Alternatively, you can manually issue commands directly, one after the

other,  at  what  is  called  the  Python  prompt.  To  run  a  Python  script  on  most  computer

systems you type within the command line interface, after the operating-system prompt, as

illustrated in

Figure 3.1

. This will generally be set up as standard on Linux and Macintosh

computers.  However,  for  Windows  care  must  be  taken  to  set  the  PATH  environment

variable,  as  illustrated  in

Figure  3.2

.  Also  for  Windows  systems,  because  the  command

line  interface  is  less  visible,  it  is  common  to  execute  a  script  by  double-clicking  on  its

icon. On-click execution can usually be set up on other systems too.

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