Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

I agree, I would not modify the file content. At present it is however not possible to use e.g. getSeq on these TwoBitFiles, since the chromosome names in the submitted GRanges (e.g. 1) do not match the seqnames/seqinfo of the TwoBitFile. I don’t know if a seqnames or seqinfo method stripping

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

That is one solution. But everyone using that genome would need to reset the seqlevels to the "standard" ones. In this specific case, is there any reason not to just use the BSgenome for GRCh38? On Fri, Jan 8, 2016 at 11:04 AM, Hervé Pagès wrote: > Hi Jo, Michael, > > What

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

On 01/08/2016 01:09 PM, Michael Lawrence wrote: That is one solution. But everyone using that genome would need to reset the seqlevels to the "standard" ones. In this specific case, is there any reason not to just use the BSgenome for GRCh38? I agree. Maybe we don't need seqlevels<-,TwoBitFile

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

Hi Jo, Michael, What about implementing a seqlevels() setter for TwoBitFile objects? All you need for this is an extra slot for storing the user-supplied seqlevels. Note that in general the seqlevels() setter allows more than renaming the seqlevels. It also allows dropping, adding, and shuffling

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

This is perhaps something that could be handled when population the hub, but I'm not sure how rtracklayer could automatically derive the chromosome names. On Fri, Jan 8, 2016 at 2:37 AM, Rainer Johannes wrote: > dear all, > > I just run into a problem with a TwoBitFile