Some scripts and stuff for personal use. If you need to copy a function. Go ahead.
BioPython is a tad lacking in some areas. It is great, but sometimes stuff needs to be done. Such as editing sequences, MutSeq isn't the friendliest. Off by one error and all the rest. Here there are a few functions that edit a sequence, you might find them useful. If I had more time I would make it prettier and donate it.
Another thing I keep seeming to have to deal with is multiple SeqRecords (genome: main chromosome and 2 plasmids) and finding a feature by its locus, which make me think that RecordList object would be appealing. Anyway. Pipedreams. Biopython is after so much better than BioPerl.
In here there are also KEGG and SBML manipulation scripts.
If you were told there is a link in an email somewhere, but nobody can find it, it is okay here are two links for you:
- Here is a copy of the protocol sheet for RNASeq analysis.
- The above link also includes a locus converter widget
- Super secret files
Uhm, it is a bit of security risk, but it futureproofs stuff. Plus, I seem to be cursed when it comes to search engine optimisation. So I doubt anyone will find this...