What Happened?

Been a while, hasn’t it? Anyways, some background context I feel is worth mentioning:

BioFlow was created for a research project of mine. Not for anything less specific, not to be used as a universal tool — though that’d be nice!

When I first made it, I realized pretty quickly that.. I’m not actually accomplishing anything for my research goal, but rather just trying to remake your generic Python Bioinformatics pipeline, which of course was not what I should focus on.

As such, you’ll notice the project in its entirety has been changed to reflect this.

The actual Changes

There’s a LOT of changes, obviously. It’s around 10 hours worth of direct coding work (not counting all of the time spent doing research, gathering data, making decisions and creating formulas, etc.), and — as per usual — I didn’t break it up into multiple devlogs.

Instead, I locked in for 4 days, and now we have:

• A computational analysis pipeline written mainly in Flower, which reads species metadata and protein annotations from TSV files, validates them, and exports candidate-family counts and normalized features. I used a C bridge for file access and numerical parsing.

• Five initial candidate categories, specifically laccase-associated proteins, manganese peroxidase, lignin peroxidase, versatile peroxidase, and cytochrome P450 candidates.

• Deduplication and conflict handling allows repeated hits and multiple annotation sources to not inflate the number of proteins counted, and proteins with competing family assignments are recorded as conflicting and excluded from the family counts.

• Proteome-size normalization, where candidate counts are expressed per 1,000 predicted proteins, whilst preserving the raw counts. Missing, zero, or inconsistent denominators produce (clearly marked!) missing values.

So yea, that’s what’s been happening. Eventually I’ll link the paper to this somehow, and of course keep the analysis pipeline open source completely for reproducible results and independent verification!

Thanks for reading, much love <3