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

Hervé Pagès hpages at fredhutch.org
Sat Jan 9 21:19:30 CET 2016


On 01/09/2016 08:42 AM, Michael Lawrence wrote:
> I can understand the desire to avoid defining and enforcing our own
> standards on third-party data: it's error-prone, potentially
> confusing, etc. But the same is even more true of expecting the user
> to perform the mapping via some adhoc approach.
>
> It's unfortunate that Ensembl does not follow the convention of naming
> their FASTA sequences by their seqlevels, but I'm not sure how
> wide-spread that convention is in the first place.

Actually, and according to https://en.wikipedia.org/wiki/FASTA_format,
it seems that:

   The word following the ">" symbol is the identifier of the sequence,
   and the rest of the line is the description (both are optional).

so Rsamtools::indexFa is doing the right thing by trimming the
description line. Maybe that's what seqinfo,TwoBitFile should do
too?

H.

>
> Why does Bioconductor distribute genomes in two different ways:
> BSgenome and via AnnotationHub? Couldn't those two distribution
> mechanisms be unified? That might mitigate some of the maintenance
> cost and better encapsulate the added complexity.
>
> Michael
>
> On Sat, Jan 9, 2016 at 8:12 AM, Morgan, Martin
> <Martin.Morgan at roswellpark.org> wrote:
>> We switched to TwoBitFile with a recent ensembl release, thinking that it had better performance and other characteristics compared to the previous FaFile.
>>
>> The 'recipe' used to create the FaFiles did not explicitly trim the label; that appears to be something done by Rsamtools::indexFa and hence (a now quite dated) version of samtools.
>>
>> I'm not precisely sure where we stand on correcting this. The original approach just takes what we're given and makes a 2bit file. At least provisionally we had decided (after Thurs / Fri exchanges) to make the seqlevels sensible on the way in to annotation hub; this is against Sean's advice and I'm not really a big fan of this.
>>
>> I like the idea of being able to dynamically remap the seqlevels when the 2bit file is loaded by AnnotationHub, which would require Herve's suggestion of settable seqlevels on TwoBitFile.
>>
>> Martin
>> ________________________________________
>> From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Rainer Johannes [Johannes.Rainer at eurac.edu]
>> Sent: Saturday, January 09, 2016 11:01 AM
>> To: Hervé Pagès
>> Cc: Michael Lawrence; Martin Morgan
>> Subject: Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub
>>
>> Yes, using BSGenome would help in this case.
>> In the long run I think it might be important to have this fixed, not necessarily for human, but for other species/genome builds for which there might not be an BSGenome package available; through AnnotationHub all GTF files and fasta files would be available. Note also that the FaFiles from Ensembl do have the “correct” chromosome names although I assume they were built from the same Ensembl fasta files than the TwoBitFiles.
>>
>> jo
>>
>>> On 08 Jan 2016, at 22:49, Hervé Pagès <hpages at fredhutch.org> wrote:
>>>
>>> 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 for that particular
>>> use case. Just wanted to mention that the ability to rename the
>>> sequences in a TwoBitFile, FastaFile, or other file-based object that
>>> supports seqinfo() would be useful in general.
>>>
>>> H.
>>>
>>>>
>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>
>>>>> --
>>>>> Hervé Pagès
>>>>>
>>>>> Program in Computational Biology
>>>>> Division of Public Health Sciences
>>>>> Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N, M1-B514
>>>>> P.O. Box 19024
>>>>> Seattle, WA 98109-1024
>>>>>
>>>>> E-mail: hpages at fredhutch.org
>>>>> Phone:  (206) 667-5791
>>>>> Fax:    (206) 667-1319
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fredhutch.org
>>> Phone:  (206) 667-5791
>>> Fax:    (206) 667-1319
>>
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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
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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