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Sorry, I was just pointing it out in case for anyone copying the code as they are both very common cases - especially dots as gap characters. The Grammar syste
by coriny 12y ago
Sorry, I was just pointing it out in case for anyone copying the code as they are both very common cases - especially dots as gap characters.
The Grammar system does look quite nice. Parsing is definitely a Perl forte - though I seriously hope bioinformatics in general will continue to abandon these crazy formats that can't be read easily by humans or machine.
- Ultimatt 12y agoYeah I would rather all the awful formats would go away. But the process of removing them tends to just birth new awful formats into existence :(
- coriny 12y agoI'm increasingly of the opinion, after having to deal with biologist data format hackery for many years (they have no shame!), that every biologist should be taught relational database normalisation. That would make them actually stop and think about the structure of the data they're recording and how to make it computationally tractable. Even more, they should not even start their experiment until they've cleared their data recording structure with a bioinformatician. Then we ban them from using flat files. Related tables or nothing. I've wasted too much time, and they're not competent enough to work with JSON/XML/Excel.