Question

I am trying to run an awk script using python, so I can process some data.

Is there any way to get an awk script to run in a python class without using the system class to invoke it as shell process? The framework where I run these python scripts does not allow the use of a subprocess call, so I am stuck either figuring out a way to convert my awk script in python, or if is possible, running the awk script in python.

Any suggestions? My awk script basically read a text file and isolate blocks of proteins that contains a specific chemical compound (the output is generated by our framework; I’ve add an example of how does it looks like below) and isolate them printing them out on a different file.

    buildProtein compoundA compoundB
    begin fusion
    Calculate : (lots of text here on multiple lines)
    (more lines)
    Final result - H20: value CO2: value Compound: value 
    Other Compounds X: Value Y: value Z:value

    [...another similar block]

So for example if I build a protein and I need to see if in the compounds I have CH3COOH in the final result line, if it does I have to take the whole block, starting from the command “buildProtein”, until the beginning of the next block; and save it on a file; and then move to the next and see if it has again the compound that I am looking for…if it does not have it I skip to the next, until the end of the file (the file has multiple occurrence of the compound that I search for, sometimes they are contiguous while other times they are alternate with blocks that has not the compound.

Any help is more than welcome; banging my head for weeks now and after finding out this site I decided to ask for some help.

Thanks in advance for your kindness!

Answer 1

If you can’t use the subprocess module, the best bet is to recode your AWK script in Python. To that end, the fileinput module is a great transition tool with and AWK-like feel.