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Debugging in Python

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Beginning the third section in our tutorial/guide, we are going to see the chapter six of BPB. This chapter discusses the topics of creating subroutines (in Python’s case functions) and debugging the code. We are going to start by the end.

In Python, code debugging can be done as in any other programming language: Perl has pdb, C/C++ has gdb, etc. Python also has a pdb module that can be imported and run to check for errors in your code. Using this command line:

python -m pdb myscript

will start the debug module and this will run your script. If you are an experienced programmer, who is just starting Python, pdb usage might look simple and straightforward. On the other hand, if you don’t have a lot of experience in programming I would suggest a different approach, as you become more comfortable with the language. Python has a great advantage over some other interpreted languages, allowing you to interactively code using the interpreter. So if your code is not working properly, maybe a wrong output or a value that is not being correctly calculated you have the options of coding the part of your script that is not working using the interpreter or use the first rule of debugging: include print statements that output the value of variables/objects. Another option is to use a Python code editor, what will also help you with highlight your code. I have little experience with Python code editors, as I normally code in Linux and use Kate. Lately I have been trying Komodo edit which is a cross-platform freeware from Active State. It looks pretty good but I never tried debugging my code with it. So, these are my advices if you are just starting to program. Maybe because of the age of Beginning Perl for Bioinformatics (published in 2001), Perl’s pdb was the only option back then. Thanks to major advances on open-source and free software there are many other options nowadays to debug your code. python -m pdb myscript