Python Programming for Biology: Bioinformatics and Beyond

Working with variable file names

When writing a program we often want it to be able work with different files on different

occasions, each with a different name or file path. Naturally it is possible to sidestep this

issue  by  simply  writing  file  paths  into  the  program  code  and  change  the  program

whenever it needs to work on a different file. However, it is often far easier to accept the

name of the file (or files) as variable arguments when we run the Python program. To do

this we could either use a graphical interface (see

Chapter 26

)  to  select  files  using  a  file

browser, or if we are running a program using the python command we can put the name

of the file argument after the name of the Python script. So, for example, here we refer to a

file  called  ‘inputFile.txt’  in  a  directory  called  ‘data/’  which  we  include  after  the  script

name when running the program:

> python programFile.py data/inputFile.txt

Note  that  the  directory  separator  ‘/’  would  be  a  backslash  ‘\’  on  Windows  systems.

Inside the programFile.py script to access the name of the file from the command line we

simply  need  to  import  sys.argv.  This  is  a  list  containing  all  of  the  text  fields  that  were

filled in on the command line, starting with the name of the Python script itself, when the

script was run:

import sys

pyScriptName = sys.argv[0] # 'programFile.py'

dataFileName = sys.argv[1] # 'data/inputFile.txt'

---

workFunction(dataFileName) # Use the file name for something…

Thus  by  accessing  sys.argv[1],  and  higher  numeric  indices  for  further  files,  we  can

define file paths (or any other parameters we want to pass to the script) in a dynamic way

when we run the program.