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

Sun Jan 10 19:28:10 CET 2016

Yes, thanks for those details, Herve. I changed rtracklayer to take
the first word as the seqlevels.

Michael

On Sun, Jan 10, 2016 at 9:50 AM, Rainer Johannes
<Johannes.Rainer at eurac.edu> wrote:
> That would be great! I don’t think we would loose any information with that behaviour. All fasta files from Ensembl have that format (id, whitespace and description). Implementing that would render the fasta files from Ensembl provided as TwoBit files via AnnotationHub usable without having to tweak the objects afterwards. I would highly appreciate that (and people working with other species than mouse/human/rat too)!
>
> jo
>
>> On 09 Jan 2016, at 21:19, Hervé Pagès <hpages at fredhutch.org> wrote:
>>
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>> This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
>>
>> --
>> 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
>