[Bioc-devel] glitches with releaseName() and seqlevelsStyle()
Robert Castelo
robert@c@@te|o @end|ng |rom up|@edu
Thu Sep 3 14:22:57 CEST 2020
Hi Hervé,
On 02/09/2020 21:44, Pages, Herve wrote:
> Hi Robert,
>
>
>
> On 9/2/20 11:12, Robert Castelo wrote:
>> hi,
>>
>> i've found the following glitches with 'releaseName()' and
>> 'seqlevelsStyle()', i guess due to recent changes in BSgenome and
>> GenomeInfoDb, which is why i'm cc'ing Hervé ;)
>>
>> ===========BioC release 3.11 everything OK=============
>> library(BSgenome.Hsapiens.UCSC.hg19)
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>>
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>>
>> releaseName(Hsapiens)
>> [1] "Genome Reference Consortium GRCh37.p13"
>> releaseName(as(Hsapiens, "GenomeDescription"))
>> [1] "Genome Reference Consortium GRCh37.p13"
>>
>> seqlevelsStyle(txdb)
>> [1] "UCSC"
>> seqlevelsStyle(txdb) <- "NCBI"
>> seqlevelsStyle(txdb)
>> [1] "NCBI" "Ensembl"
>> head(seqlengths(txdb))
>> 1 2 3 4 5 6
>> 249250621 243199373 198022430 191154276 180915260 171115067
>> =======================================================
>>
>> ============BioC devel 3.12 inconsistencies============
>> library(BSgenome.Hsapiens.UCSC.hg19)
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>>
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>>
>> releaseName(Hsapiens)
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function ‘releaseName’ for
>> signature ‘"BSgenome"’
>> releaseName(as(Hsapiens, "GenomeDescription"))
>> [1] NA
>>
>> seqlevelsStyle(txdb)
>> [1] "UCSC"
>> seqlevelsStyle(txdb) <- "NCBI"
>> seqlevelsStyle(txdb)
>> [1] "NCBI" "UCSC"
>> head(seqlengths(txdb))
>> 1 2 3 4 5 6
>> 249250621 243199373 198022430 191154276 180915260 171115067
>> ========================================================
>>
>> in the case of 'releaseName()' i interpret that the method has become
>> defunct for 'BSgenome' objects, but i think it should give a sensible
>> result with a 'GenomeDescription' object, so something may be going
>> wrong with the coercion from 'BSgenome' to 'GenomeDescription'.
> I'm dropping the notion of "release name" for BSgenome objects in BioC
> 3.12. For backward compatibility I just restored a temporary
> releaseName() method (in BSgenome 1.57.6) that does the following:
>
> > releaseName(BSgenome.Hsapiens.UCSC.hg19)
> [1] NA
> Warning message:
> Starting with Bioconductor 3.12, BSgenome objects no longer have a
> "release name". As a consequence of this change calling releaseName()
> on a BSgenome object now always returns NA and is deprecated.
>
ah ok, i see, this is fine, but the purpose of the 'releaseName()'
function in the documentation is confusing, 'help(releaseName)' says:
‘releaseName(x)’: Return the release name of this genome, which is
generally made of the name of the organization who assembled
it plus its Build version. For example, UCSC uses ‘"hg18"’
for the version of the Human genome corresponding to the
Build 36.1 from NCBI hence the release name for this genome
is ‘"NCBI Build 36.1"’.
but, if i'm interpreting you correctly, genomes in BSgenome.* packages
have no release name anymore. maybe the help page of 'releaseName',
which is the one of the 'GenomeDescription' class should say only:
'releaseName(x)': Return the release name of 'x'.
for whatever 'x' may be and whatever a release name may mean.
>> in the case of 'seqlevelsStyle()', while the change of style seems to
>> happen, i don't see how the style can be simultaneously NCBI and UCSC.
> This happens when you end up with a mix of styles. In the case of hg19,
> all the sequences get renamed from UCSC to NCBI names **except** chrM:
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>
> table(genome(txdb))
> # hg19
> # 93
>
> seqlevelsStyle(txdb) <- "NCBI"
>
> seqlevelsStyle(txdb)
> # [1] "NCBI" "UCSC"
>
> table(genome(txdb))
> # GRCh37.p13 hg19
> # 92 1
>
> genome(txdb)[genome(txdb) == "hg19"]
> # chrM
> # "hg19"
>
> chrM cannot and should not be renamed to MT because the MT sequence in
> GRCh37.p13 is NOT the same as the chrM sequence in hg19. So the new
> seqlevelsStyle() behavior fixes a long standing bug.
>
> See previous discussion on this list about the long dance between UCSC
> and NCBI about the mitochondrian sequence in hg19/GRCh37/GRCh37.p13:
> https://stat.ethz.ch/pipermail/bioc-devel/2020-August/017086.html
>
> Hope this helps,
> H.
i see, this makes sense, i've followed the discussion about the
mitochondrian sequence naming, but didn't connect it with this behavior.
i'd like to set the sequence style of a TxDb object to whatever the
sequence style is of the BSgenome object, dropping the levels in the
TxDb object that are not common to the BSgenome object (removing the
mitochondrial chromosome in the case of hg19/GRCh37), so that the TxDb
object has a single sequence style, i thought this would work but i get
an error:
library(BSgenome.Hsapiens.1000genomes.hs37d5)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
bsgenome <- hs37d5
seqlevelsStyle(txdb) <- seqlevelsStyle(bsgenome)
Warning message:
In .normarg_seqlevelsStyle(value) :
more than one seqlevels style supplied, using the 1st one only
seqlevelsStyle(txdb)
[1] "NCBI" "UCSC"
commonChr <- intersect(seqlevels(txdb), seqlevels(bsgenome))
commonChr
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13"
"14" "15"
[16] "16" "17" "18" "19" "20" "21" "22" "X" "Y"
txdb <- keepSeqlevels(txdb, commonChr)
seqlevelsStyle(txdb)
Error in .normarg_genome(value, seqnames(x)) :
when length of supplied 'genome' vector is not 1, then it must equal
the number of sequences
traceback()
9: stop(wmsg("when length of supplied 'genome' vector is not 1, ",
"then it must equal the number of sequences"))
8: .normarg_genome(value, seqnames(x))
7: `genome<-`(`*tmp*`, value = x$user_genome)
6: `genome<-`(`*tmp*`, value = x$user_genome)
5: seqinfo(x)
4: seqinfo(x)
3: seqlevelsStyle(seqinfo(x))
2: seqlevelsStyle(txdb)
1: seqlevelsStyle(txdb)
i guess this should have worked, right?
thanks!
robert.
>> below my session information for the BioC devel 3.12 version.
>>
>> thanks!!
>>
>> robert.
>>
>> sessionInfo()
>> R version 4.0.0 (2020-04-24)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 18.04.4 LTS
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
>> [2] GenomicFeatures_1.41.2
>> [3] AnnotationDbi_1.51.3
>> [4] Biobase_2.49.0
>> [5] BSgenome.Hsapiens.UCSC.hg19_1.4.3
>> [6] BSgenome_1.57.5
>> [7] rtracklayer_1.49.5
>> [8] Biostrings_2.57.2
>> [9] XVector_0.29.3
>> [10] GenomicRanges_1.41.6
>> [11] GenomeInfoDb_1.25.10
>> [12] IRanges_2.23.10
>> [13] S4Vectors_0.27.12
>> [14] BiocGenerics_0.35.4
>> [15] BiocManager_1.30.10
>>
>> loaded via a namespace (and not attached):
>> [1] SummarizedExperiment_1.19.6 progress_1.2.2
>> [3] tidyselect_1.1.0 purrr_0.3.4
>> [5] lattice_0.20-41 generics_0.0.2
>> [7] vctrs_0.3.1 BiocFileCache_1.13.1
>> [9] blob_1.2.1 XML_3.99-0.4
>> [11] rlang_0.4.6 pillar_1.4.4
>> [13] glue_1.4.1 DBI_1.1.0
>> [15] rappdirs_0.3.1 BiocParallel_1.23.2
>> [17] bit64_0.9-7.1 dbplyr_1.4.4
>> [19] matrixStats_0.56.0 GenomeInfoDbData_1.2.3
>> [21] lifecycle_0.2.0 stringr_1.4.0
>> [23] zlibbioc_1.35.0 memoise_1.1.0
>> [25] biomaRt_2.45.2 curl_4.3
>> [27] Rcpp_1.0.4.6 openssl_1.4.1
>> [29] DelayedArray_0.15.7 bit_1.1-15.2
>> [31] Rsamtools_2.5.3 hms_0.5.3
>> [33] askpass_1.1 digest_0.6.25
>> [35] stringi_1.4.6 dplyr_1.0.0
>> [37] grid_4.0.0 tools_4.0.0
>> [39] bitops_1.0-6 magrittr_1.5
>> [41] RCurl_1.98-1.2 RSQLite_2.2.0
>> [43] tibble_3.0.1 crayon_1.3.4
>> [45] pkgconfig_2.0.3 ellipsis_0.3.1
>> [47] Matrix_1.2-18 prettyunits_1.1.1
>> [49] assertthat_0.2.1 httr_1.4.1
>> [51] R6_2.4.1 GenomicAlignments_1.25.3
>> [53] compiler_4.0.0
>>
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