[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
them. But you don't need to support all that. Supporting renaming would
already go a long way. See selectMethod("seqlevels<-", "TxDb") in
GenomicFeatures for an example of a restricted "seqlevels<-" method.

H.


On 01/08/2016 09:50 AM, Rainer Johannes wrote:

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 of all
but the first name-part would help here...

jo

On 08 Jan 2016, at 15:18, Sean Davis <seandavi at gmail.com> wrote:

I will make the small editorial comment to guard against modifying file
content on transit into the hub object. On the client side (after getting
such an object) I think a ?fix? would be to have a quick seqnames method to
strip off all but the first whitespace delimited piece.

Sean

On Jan 8, 2016, at 8:40 AM, Michael Lawrence <lawrence.michael at gene.com>
wrote:

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
<Johannes.Rainer at eurac.edu> wrote:

dear all,

I just run into a problem with a TwoBitFile I fetched from
AnnotationHub. I was fetching a TwoBitFile with the genomic DNA sequence, as
provided by Ensembl:

library(AnnotationHub)
ah <- AnnotationHub()
tbf <- ah[["AH50068?]]

head(seqnames(seqinfo(tbf)))

[1] "1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF"
[2] "10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF"
[3] "11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF"
[4] "12 dna:chromosome chromosome:GRCh38:12:1:133275309:1 REF"
[5] "13 dna:chromosome chromosome:GRCh38:13:1:114364328:1 REF"
[6] "14 dna:chromosome chromosome:GRCh38:14:1:107043718:1 REF"

Would be nice, if the seqnames would be really just the chromsome names
and not the whole string from the FA file header. Is there a way I could fix
the file myself or is this something that should be fixed in the rtracklayer
or AnnotationHub package when the TwoBitFile is created?

thanks, jo

--
Herv? Pag?s

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