Command line input

Avoiding hard-coding
Command line arguments
- Providing command line arguments
- Accessing command line arguments
Checking the number of arguments

Avoiding hard-coding

Up to this point, we have been hard-coding many elements in the code. For example, in get_gene_coords.py, we explicitly provide the file name for the genes of interest. This is problematic because if we want to extract coordinates from another file, we have to change the source code itself.

Command line arguments

A better way to do this is to provide this information as input the program.

Providing command line arguments

To provide input to a program at run time, additional arguments can be given after the program name.

$ python program arg1 arg2 ...

Note: The $ above is often used to indicate that the command is being given at the command line (in the terminal or Windows Command Prompt).

For get_gene_coords.py, this would look like this:

$ python get_gene_coords.py ../data/genes-5random.txt

First, we provide the name of the script to run, and then we provide the path to the file containing the genes of interest as an argument to the script.

Accessing command line arguments

Now that we have given the argument to the program, we have to write code that makes use of it. To do this, we need to import a module, sys.

import sys

sys contains a list, named argv, that has information about the command line arguments.

Make a script (name it argtest.py) that imports the sys module and then prints argv.

import sys
print(sys.argv)

['']

Now test it from the command line.

$ python argtest.py

This should print a list that contains "argtest.py". Now try to pass an argument.

$ python argtest.py somearg

This should print the script name as above, but the list should contain a second string, "somearg". Each additional argument will be added to the list.

We can apply this to get_gene_coords.py example. Before, we were explicitly declaring the file name.

gene_file = 'data/genes-5random.txt'

Instead, we can do this:

import sys
gene_file = sys.argv[1]
## rest of script ...

This allows any file that has the correct format (in this case, one gene name per line) to be given as input to the script.

$ python get_gene_coords.py newfile

Checking the number of arguments

If something seems wrong with the input arguments, it is often a good idea to stop the program and print a helpful usage message. A simple (and good) thing to check is whether the right number of arguments has been given. For example, get_gene_coords.py needs exactly one argument to work properly. What code could you write to check that the correct number of arguments has been passed?