[Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?
On 06/05/2015 11:43 AM, Michael Lawrence wrote:
On Thu, Jun 4, 2015 at 11:48 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:
I also think that we're heading towards something like that.
So genome(gr) <- "hg19" would:
(a) Add any missing information to the seqinfo.
(b) Sort the seqlevels in "canonical" order.
(c) Change the seqlevels style to UCSC style if they are not.
The 3 tasks are orthogonal. I guess most of the times people want
an easy way to perform them all at once.
We could easily support (a) and (b). This assumes that the current
seqlevels are already valid hg19 seqlevels:
si1 <- Seqinfo(c("chrX", "chrUn_gl000249", "chr2", "chr6_cox_hap2"))
gr1 <- GRanges(seqinfo=si1)
hg19_si <- Seqinfo(genome="hg19")
## (a):
seqinfo(gr1) <- merge(seqinfo(gr1), hg19_si)[seqlevels(gr1)]
seqinfo(gr1)
# Seqinfo object with 4 sequences (1 circular) from hg19 genome:
# seqnames seqlengths isCircular genome
# chrX 155270560 FALSE hg19
# chrUn_gl000249 38502 FALSE hg19
# chr2 243199373 FALSE hg19
# chr6_cox_hap2 4795371 FALSE hg19
## (b):
seqlevels(gr1) <- intersect(seqlevels(hg19_si), seqlevels(gr1))
seqinfo(gr1)
# Seqinfo object with 4 sequences (1 circular) from hg19 genome:
# seqnames seqlengths isCircular genome
# chr2 243199373 FALSE hg19
# chrX 155270560 FALSE hg19
# chr6_cox_hap2 4795371 FALSE hg19
# chrUn_gl000249 38502 FALSE hg19
(c) is harder because seqlevelsStyle() doesn't know how to rename
scaffolds yet:
si2 <- Seqinfo(c("X", "HSCHRUN_RANDOM_CTG42", "2", "HSCHR6_MHC_COX_CTG1"))
gr2 <- GRanges(seqinfo=si2)
seqlevelsStyle(gr2)
# [1] "NCBI"
seqlevelsStyle(gr2) <- "UCSC"
seqlevels(gr2)
# [1] "chrX" "HSCHRUN_RANDOM_CTG42" "chr2"
# [4] "HSCHR6_MHC_COX_CTG1"
So we need to work on this.
I'm not sure about using genome(gr) <- "hg19" for this. Right now
it sets the genome column of the seqinfo with the supplied string
and nothing else. Aren't there valid use cases for this?
Not sure. People would almost always want the seqname style and order to be consistent with the given genome.
Agreed but my worry is that when they don't, then they would be left with no way to just set the genome column. H.
What about using seqinfo(gr) <- "hg19" instead? It kind of suggests that the whole seqinfo component actually gets filled.
Yea, but "genome" is so intuitive compared to "seqinfo".
H. On 06/04/2015 06:30 PM, Tim Triche, Jr. wrote:
that's kind of always been my goal... Statistics is the grammar of science. Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> On Thu, Jun 4, 2015 at 6:29 PM, Michael Lawrence <lawrence.michael at gene.com <mailto:lawrence.michael at gene.com>> wrote: Maybe this could eventually support setting the seqinfo with: genome(gr) <- "hg19" Or is that being too clever? On Thu, Jun 4, 2015 at 4:28 PM, Herv? Pag?s <hpages at fredhutch.org <mailto:hpages at fredhutch.org>> wrote:
> 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 <mailto: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 <mailto: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
>>>>
>>>> On Wed, Jun 3, 2015 at 12:17 PM, Vincent Carey
>>>> <stvjc at channing.harvard.edu <mailto: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
<mailto: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 <mailto: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
>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
mailing list
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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mailing list
>>
>>
>> _______________________________________________
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>
> --
> Herv? Pag?s
>
> 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 <mailto:hpages at fredhutch.org>
> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>
> _______________________________________________
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-- Herv? Pag?s 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
Herv? Pag?s 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