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"Often a regexp can match in many ways ..." When I worked in bioinformatics, some 20 years ago, I implemented a SWISS-PROT to regex converter. I ended up havin
by dalke 7y ago
"Often a regexp can match in many ways ..."
When I worked in bioinformatics, some 20 years ago, I implemented a SWISS-PROT to regex converter. I ended up having to ask SWISS-PROT was if certain patterns were meant to be greedy or lazy, since the documentation wasn't clear. I've since forgotten the answer, but I have a vague memory that they hadn't really considered that multiple interpretations were possible, so they probably expected greedy matches.
- hoytech 7y agoInteresting, thanks!
- jerven 7y agoParsing the flatfile of Swiss-Prot in detail is the best way to lose your sanity ;) I know because that is part of my day job. It's gotten better but I highly recommend you either use the RDF or XML. The flatfile looks easy but is an endless source of bugs and urgent changes.
- dalke 7y agoI did say it was 20 years ago. ;) Since then I've been working in cheminformatics. Which has its own forms of insanity.
- jerven 7y agoCan I just say that these day's you can search Swiss-Prot with InchiKey's due to our integration with rhea (https://www.uniprot.org/news/2018/12/05/release https://www.uniprot.org/news/2018/12/05/release)