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

[Michael Lawrence]

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 <hpages at fredhutch.org> wrote:
> 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
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>> _______________________________________________
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>>>
>>>
>>
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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>
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