Python Programming for Biology: Bioinformatics and Beyond

Figure 3.2.  Setting the PATH environment variable in Windows. For the ‘python’

command to be recognised by Windows systems the PATH environment variable must

include the location of the directory that contains the ‘python.exe’ file. An environment

variable may be set in the Windows graphical interface via Control Panel

→ System and

Security

→ System → Advanced system settings. If PATH is not already defined then the

Python executable location may be specified via New …, for example, as ‘C:\Python27’

or ‘C:\Python33’, depending on the version. If the PATH is already defined then, after

selection of this system variable in the lower table, using Edit … enables the addition of

the Python location after any existing values, after a semicolon, for example, adding

‘;C:\Python34’. Note that the PATH specification has no spaces between entries (only ‘;’)

and no trailing slash ‘\’.

The file name for Python scripts traditionally ends in ‘.py’, as illustrated in the example

below, although strictly speaking it does not have to. By running the script we send the file

containing lines of code to the Python interpreter, which reads it and acts on the contents.

Also, if required, a script can have input values called arguments passed along when it is

run, as illustrated for the Linux, UNIX or Mac command line:

> python scriptName.py argument1 argument2

This  assumes  that  the  executed  ‘python’  command  is  on  your  search  path,  where  the

operating system knows to look for commands; otherwise you have to type the full path to

its location.

The alternative to running Python from script files is to run Python alone, without a file,

in an interactive mode. This mode gives you a prompt ‘>>>’, where you can type manual

input  that  is  passed  to  the  interpreter  one  line  at  a  time.  To  start  the  interpreter  with  the

Windows operating system you would click on the Python icon. To start from Mac OS X,

Linux  or  UNIX  this  means  opening  a  command-line  shell  and  typing  ‘python’,  then

pressing the Return or Enter key.

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You can type commands at this prompt, pressing the Return or Enter key to issue each

command and move on to the next line. Note that, by using the ‘-i’ flag, it is also possible

to run a Python script and then go into an interactive mode immediately afterwards. When

the script is done it presents you with the prompt and awaits further instructions:

> python -i scriptName.py

[ Output of the script ]

>>>

When you are done, you quit by typing either the Ctrl-d key combination (so hold the

‘Ctrl’ key down and then tap the ‘d’ key) for Mac, Linux and UNIX systems or Ctrl-z for

Windows  systems.  The  Python  prompt  is  convenient  for  testing  out  simple  bits  of  code.

More serious work is normally done with scripts, however. In this chapter you can work

either way.

In  Python  2  you  can  print  a  text  message  to  the  terminal  window  via  the  print

command, for example:

print 'Hello world'

This  automatically  moves  onto  the  next  line  because  it  prints  a  newline  control

character at the end. However, if you do not want to go to the next line put a comma at the

end:

print 'Hello world',

In Python 3 the print statement changes to a function, which in simple terms means that

it requires parentheses:

print('Hello world')

This  function  is  also  available  in  Python  2,  although  it  doesn’t  print  as  nicely  as  in

Python 3.

2

The Python 2 syntax for print is fairly ubiquitous in existing Python code. For

new code it is probably best to use the Python 3 syntax, even when using Python 2. In this

book we will use the print function rather than the print statement.

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