[Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?

Hervé Pagès hpages at fredhutch.org
Fri Jun 5 01:28:38 CEST 2015 

Hi,

FWIW I started to work on supporting quick generation of a standalone
Seqinfo object via Seqinfo(genome="hg38") in GenomeInfoDb.

It already supports hg38, hg19, hg18, panTro4, panTro3, panTro2,
bosTau8, bosTau7, bosTau6, canFam3, canFam2, canFam1, musFur1, mm10,
mm9, mm8, susScr3, susScr2, rn6, rheMac3, rheMac2, galGal4, galGal3,
gasAcu1, danRer7, apiMel2, dm6, dm3, ce10, ce6, ce4, ce2, sacCer3,
and sacCer2. I'll add more.

See ?Seqinfo for some examples.

Right now it fetches the information from internet every time you
call it but maybe we should just store that information in the
GenomeInfoDb package as Tim suggested?

H.

On 06/03/2015 12:54 PM, Tim Triche, Jr. wrote:
> That would be perfect actually.  And it would radically reduce & modularize maintenance.  Maybe that's the best way to go after all.  Quite sensible.
>
> --t
>
>> On Jun 3, 2015, at 12:46 PM, Vincent Carey <stvjc at channing.harvard.edu> wrote:
>>
>> It really isn't hard to have multiple OrganismDb packages in place -- the
>> process of making new ones is documented and was given as an exercise in
>> the EdX course.  I don't know if we want to institutionalize it and
>> distribute such -- I think we might, so that there would be Hs19, Hs38,
>> mm9, etc. packages.  They have very little content, they just coordinate
>> interactions with packages that you'll already have.
>>
>> On Wed, Jun 3, 2015 at 3:26 PM, Tim Triche, Jr. <tim.triche at gmail.com>
>> wrote:
>>
>>> Right, I typically do that too, and if you're working on human data it
>>> isn't a big deal.  What makes things a lot more of a drag is when you work
>>> on e.g. mouse data (mm9 vs mm10, aka GRCm37 vs GRCm38) where Mus.musculus
>>> is essentially a "build ahead" of Homo.sapiens.
>>>
>>> R> seqinfo(Homo.sapiens)
>>> Seqinfo object with 93 sequences (1 circular) from hg19 genome
>>>
>>> R> seqinfo(Mus.musculus)
>>> Seqinfo object with 66 sequences (1 circular) from mm10 genome:
>>>
>>> It's not as explicit as directly assigning the seqinfo from a genome that
>>> corresponds to that of your annotations/results/whatever.  I know we could
>>> all use crossmap or liftOver or whatever, but that's not really the same,
>>> and it takes time, whereas assigning the proper seqinfo for relationships
>>> is very fast.
>>>
>>> That's all I was getting at...
>>>
>>>
>>> Statistics is the grammar of science.
>>> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
>>>
>>> On Wed, Jun 3, 2015 at 12:17 PM, Vincent Carey <stvjc at channing.harvard.edu
>>>> wrote:
>>>
>>>> I typically get this info from Homo.sapiens.  The result is parasitic
>>>> on
>>>> the TxDb that is in there.  I don't know how easy it is to swap alternate
>>>> TxDb in to get a different build.  I think it would make sense to regard
>>>> the OrganismDb instances as foundational for this sort of structural data.
>>>>
>>>> On Wed, Jun 3, 2015 at 3:12 PM, Kasper Daniel Hansen <
>>>> kasperdanielhansen at gmail.com> wrote:
>>>>
>>>>> Let me rephrase this slightly.  From one POV the purpose of GenomeInfoDb
>>>>> is
>>>>> clean up the seqinfo slot.  Currently it does most of the cleaning, but
>>>>> it
>>>>> does not add seqlengths.
>>>>>
>>>>> It is clear that seqlengths depends on the version of the genome, but I
>>>>> will argue so does the seqnames.  Of course, for human, chr22 will not
>>>>> change.  But what about the names of all the random contigs?  Or for
>>>>> other
>>>>> organisms, what about going from a draft genome with 10k contigs to a
>>>>> more
>>>>> completely genome assembled into fewer, larger chromosomes.
>>>>>
>>>>> I acknowledge that this information is present in the BSgenome packages,
>>>>> but it seems (to me) to be very appropriate to have them around for
>>>>> cleaning up the seqinfo slot.  For some situations it is not great to
>>>>> depend on 1 GB> download for something that is a few bytes.
>>>>>
>>>>> Best,
>>>>> Kasper
>>>>>
>>>>> On Wed, Jun 3, 2015 at 3:00 PM, Tim Triche, Jr. <tim.triche at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> It would be nice (for a number of reasons) to have chromosome lengths
>>>>>> readily available in a foundational package like GenomeInfoDb, so that,
>>>>>> say,
>>>>>>
>>>>>> data(seqinfo.hg19)
>>>>>> seqinfo(myResults) <- seqinfo.hg19[ seqlevels(myResults) ]
>>>>>>
>>>>>> would work without issues.  Is there any particular reason this
>>>>> couldn't
>>>>>> happen for the supported/available BSgenomes?  It would seem like a
>>>>> simple
>>>>>> matter to do
>>>>>>
>>>>>> R> library(BSgenome.Hsapiens.UCSC.hg19)
>>>>>> R> seqinfo.hg19 <- seqinfo(Hsapiens)
>>>>>> R> save(seqinfo.hg19,
>>>>>> file="~/bioc-devel/GenomeInfoDb/data/seqinfo.hg19.rda")
>>>>>>
>>>>>> and be done with it until (say) the next release or next released
>>>>>> BSgenome.  I considered looping through the following BSgenomes
>>>>> myself...
>>>>>> and if it isn't strongly opposed by (everyone) I may still do exactly
>>>>>> that.  Seems useful, no?
>>>>>>
>>>>>> e.g. for the following 42 builds,
>>>>>>
>>>>>> grep("(UCSC|NCBI)", unique(gsub(".masked", "", available.genomes())),
>>>>>> value=TRUE)
>>>>>> [1] "BSgenome.Amellifera.UCSC.apiMel2"
>>>>> "BSgenome.Btaurus.UCSC.bosTau3"
>>>>>>
>>>>>> [3] "BSgenome.Btaurus.UCSC.bosTau4"
>>>>> "BSgenome.Btaurus.UCSC.bosTau6"
>>>>>>
>>>>>> [5] "BSgenome.Btaurus.UCSC.bosTau8"      "BSgenome.Celegans.UCSC.ce10"
>>>>>>
>>>>>> [7] "BSgenome.Celegans.UCSC.ce2"         "BSgenome.Celegans.UCSC.ce6"
>>>>>>
>>>>>> [9] "BSgenome.Cfamiliaris.UCSC.canFam2"
>>>>>> "BSgenome.Cfamiliaris.UCSC.canFam3"
>>>>>> [11] "BSgenome.Dmelanogaster.UCSC.dm2"
>>>>>> "BSgenome.Dmelanogaster.UCSC.dm3"
>>>>>> [13] "BSgenome.Dmelanogaster.UCSC.dm6"
>>>>> "BSgenome.Drerio.UCSC.danRer5"
>>>>>>
>>>>>> [15] "BSgenome.Drerio.UCSC.danRer6"
>>>>> "BSgenome.Drerio.UCSC.danRer7"
>>>>>>
>>>>>> [17] "BSgenome.Ecoli.NCBI.20080805"
>>>>>> "BSgenome.Gaculeatus.UCSC.gasAcu1"
>>>>>> [19] "BSgenome.Ggallus.UCSC.galGal3"
>>>>> "BSgenome.Ggallus.UCSC.galGal4"
>>>>>>
>>>>>> [21] "BSgenome.Hsapiens.NCBI.GRCh38"      "BSgenome.Hsapiens.UCSC.hg17"
>>>>>>
>>>>>> [23] "BSgenome.Hsapiens.UCSC.hg18"        "BSgenome.Hsapiens.UCSC.hg19"
>>>>>>
>>>>>> [25] "BSgenome.Hsapiens.UCSC.hg38"
>>>>>> "BSgenome.Mfascicularis.NCBI.5.0"
>>>>>> [27] "BSgenome.Mfuro.UCSC.musFur1"
>>>>> "BSgenome.Mmulatta.UCSC.rheMac2"
>>>>>>
>>>>>> [29] "BSgenome.Mmulatta.UCSC.rheMac3"
>>>>> "BSgenome.Mmusculus.UCSC.mm10"
>>>>>>
>>>>>> [31] "BSgenome.Mmusculus.UCSC.mm8"        "BSgenome.Mmusculus.UCSC.mm9"
>>>>>>
>>>>>> [33] "BSgenome.Ptroglodytes.UCSC.panTro2"
>>>>>> "BSgenome.Ptroglodytes.UCSC.panTro3"
>>>>>> [35] "BSgenome.Rnorvegicus.UCSC.rn4"
>>>>> "BSgenome.Rnorvegicus.UCSC.rn5"
>>>>>>
>>>>>> [37] "BSgenome.Rnorvegicus.UCSC.rn6"
>>>>>> "BSgenome.Scerevisiae.UCSC.sacCer1"
>>>>>> [39] "BSgenome.Scerevisiae.UCSC.sacCer2"
>>>>>> "BSgenome.Scerevisiae.UCSC.sacCer3"
>>>>>> [41] "BSgenome.Sscrofa.UCSC.susScr3"
>>>>> "BSgenome.Tguttata.UCSC.taeGut1"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Am I insane for suggesting this?  It would make things a little easier
>>>>> for
>>>>>> rtracklayer, most SummarizedExperiment and SE-derived objects, blah,
>>>>> blah,
>>>>>> blah...
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> --t
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Statistics is the grammar of science.
>>>>>> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>     [[alternative HTML version deleted]]
>>
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>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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