Nicholas Ingolia <n...@ingolia.org> writes: > I just uploaded seqloc-0.1 to Hackage. This package is a useful > library for manipulating "sequence locations", which I use principally > for handling gene annotations.
Nice, I'm going to have to look at genome annotation RSN, so this is arriving at exactly the right moment. Thanks! > It's related to the sequence location > code that I submitted to the bio library--that code has since > bitrotted. Presumably this means that the relevant modules can be removed from bio? Or does any software depend on them? > I have a related package to work with data files in GTF and BED format > that I plan to polish up sometime soon. I've been wanting a more general way of dealing with alignments. For sequences, there's a bunch of formats that are all handled, more or less, by the same datatype. Alignments formats tend to have a wider variety of provided information - but perhaps we can build something general (an AlignLike typeclass? :-) from SeqLoc? In bio, there are parsers for Blast XML and PSL, at least. > I think the SeqLike typeclass in the module should provide a pretty > nice interface for many different sequence data type implementations. Yes, this sounds nice. > http://www.ingolia-lab.org/software/seqloc Your site is a bit short on links - is the code itself available somewhere? -k PS: I think you mentioned a BAM parser at one point, is that available somewhere? -- If I haven't seen further, it is by standing in the footprints of giants _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
