Hi all, I'm doing research before building a lightweight tool to help with common bioinformatics pain points, and I'd love your input. What's the one task you find yourself doing repeatedly that feels like it should already be automated but isn't, or the existing tools are too clunky/overkill? Could be anything: file format headaches, QC reporting, sample tracking, annotation steps, report generation, environment setup whatever costs you the most time. I'm not selling anything just trying to understand where the real friction is before writing a single line of code. All responses genuinely helpful, even a one liner.
Thanks in advance.
1 answer
Hi there! I appreciate this question because as a master's student with a background in molecular biology and only now learning to code, I deeply value heavily commented code not only for debugging purposes and clarity, but also for learning new things. Despite many instructors in intro programming classes drilling into their students the value of clear, concise code commenting and full dosctrings are often forsaken as scripts grow in length because people "get tired of scrolling back and forth" (which I happen to think is a pretty lame excuse). I have also had instructors say that if our code needs comments, it needs to be rewritten for clarity, which I do not agree with either, especially because learning to code is literally like learning a new language- its A LOT to take in to become a truly efficient programmer. When learned from the start, concise yet thorough commenting becomes second nature- it has never been a burden for me and I find myself appreciating even my own comments to re-orient myself upon returning to an old script. But there are always going to be those who dont understand the importance and value of comments. It would be awesome to have a python package dedicated to implementing concise commenting, it could even be tuned to the writer's preferred level of detail- inline, block comments, or dosctrings only- as of now, you can have a gen AI agent shadowing as you write, but wouldnt it be nice for those who complain about the length to be able to run a program at the end that adds the comments in? Perhaps that would satisfy, dare I say, everyone? and could certainly make debugging someone else's code much less grueling!
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