Using helper scripts to make bioinformatics analysis easier to maintain
February 29th, 2008One of the differences between researching a scientific problem using a computer, and developing software, is the approach to writing code. If you’re producing a bioinformatics application there is more emphasis on generating high quality, flexible code, as this makes future maintenance easier. On the other hand if you’re trying to find the answer to a biological question using a series of scripts, then the focus is on the results, rather than the standard of code. During my work, the number of scripts I have tends to grow quickly, and this leads to problems with maintaining dependencies across scripts. Examples of this can be database connection parameters, or the file system location of a library I’m calling. This is because the fastest way to get this information into a script, is to cut and paste from an already existing one. However this becomes difficult to manage, when something changes, because I have to go back through all my scripts and update each in turn.