[Bioc-devel] VariantAnnotation::readVcf() sets the wrong seqlevelsStyle in devel
Manders-2, F.M.
F@M@M@nder@ @end|ng |rom pr|n@e@m@x|m@centrum@n|
Fri Aug 7 13:43:34 CEST 2020
Hi Herve,
The performance of seqlevelStyle when the genome of a GRanges object has been set, still seems strange to me.
Here is some example code I ran in the Bioconductor:devel docker:
gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))
genome(gr) <- "hg19"
seqlevelsStyle(gr) <- "NCBI"
This results in R freezing for more than a minute, after which the following cryptic error is given:
Error in function (type, msg, asError = TRUE) :
Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Connection refused
Maybe seqlevelsStyle should check if the genome of a GRanges object has been set and throw an informative error?
With kind regards,
Freek Manders
On 06/08/2020, 19:18, "Bioc-devel on behalf of Hervé Pagès" <bioc-devel-bounces using r-project.org on behalf of hpages using fredhutch.org> wrote:
Hi Robert,
Yes seqlevelsStyle's new behavior is slightly different and less
forgiving. The thing is that it will generally reveal dormant issues
which is not such a bad thing after all.
Note that it doesn't seem completely straightforward to retrieve the
reference genome/assembly directly from the VCF header. AFAICT this
information is either missing or weirdly formatted. For example the
headers of the 1000genomes VCF files located at
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/
contain
##reference=1000Genomes-NCBI37
or in the ex2.vcf file included in VariantAnnotation it's:
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
so not clear that importing this in the genome field of the returned VCF
object would be that helpful.
Thanks for pointing me to the VariantAnnotation vignette. I'll fix the
calls to readVcf() to use GRCh37 instead of hg19. Seems like one call
(on ex2.vcf) is using the wrong genome: ex2.vcf is based on hg18/NCBI36,
not on hg19/GRCh37. Will fix that too.
Sure readVcf() could probably be improved to perform some sanity checks
by making sure that the user-supplied genome is compatible with the
chromosome names. However that still won't prevent the user from
specifying the wrong genome (e.g. GRCh37 instead of NCBI36) like in the
ex2.vcf case. Anyway this is a feature request for readVcf().
In the end I'm not sure what's the purpose of specifying the genome
anyway. What does it give us? Maybe the vignette and examples in
VariantAnnotation should stop doing that? Better to not specify the
genome than specifying the wrong one.
Best,
H.
On 8/6/20 07:42, Robert Castelo wrote:
> hi Hervé,
>
> thank you very much for your clarifications, but this behavior is
> different in release and has been different until now, this is BioC 3.11:
>
> library(VariantAnnotation)
>
> fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> seqlevels(vcf)
> [1] "22"
> seqlevelsStyle(vcf)
> [1] "NCBI" "Ensembl"
>
> i appreciate that the behavior now in devel is more consistent, i
> actually never understood the need to specify the 'genome="hg19"'
> argument since this in principle can be figured out from the VCF header
> information. However, the documentation has become right now confusing,
> if you go to subsection 2.1 and 2.1.2 from the introductory vignette, it
> shows using readVcf() with "hg19" but then the sequence names are
> literally what they are in the VCF file (NCBI style)
>
> because of the large user base of VariantAnnotation (top-49 download)
> and the many possible reverse dependencies downstream, i'd suggest that
> either readVcf() issues an error or, maybe even better, overrides the
> sequence level style in the VCF file maybe with a warning, when the
> 'genome' argument does not match the sequence style of the VCF file.
>
> cheers,
>
> robert.
>
>
> On 04/08/2020 18:29, Hervé Pagès wrote:
>> Hi Robert,
>>
>> The VCF file uses "22" for the chromosome name which is the name used
>> by NCBI. So explicitly specifying "hg19" in the readVcf() call is like
>> saying that this chromosome name is a UCSC name which is why
>> seqlevelsStyle() gets confused later.
>>
>> If you specify the name of the NCBI assembly, things work as expected:
>>
>> fl <- system.file("extdata", "chr22.vcf.gz",
>> package="VariantAnnotation")
>> vcf <- readVcf(fl, "GRCh37")
>> seqlevels(vcf)
>> # [1] "22"
>> seqlevelsStyle(vcf)
>> # [1] "NCBI"
>> seqlevelsStyle(vcf) <- "UCSC"
>> seqlevels(vcf)
>> # [1] "chr22"
>>
>> Or, if you don't know what reference genome the file is based on,
>> don't specify it:
>>
>> fl <- system.file("extdata", "chr22.vcf.gz",
>> package="VariantAnnotation")
>> vcf <- readVcf(fl)
>> seqlevels(vcf)
>> # [1] "22"
>> seqlevelsStyle(vcf)
>> # [1] "NCBI" "Ensembl"
>> seqlevelsStyle(vcf) <- "UCSC"
>> seqlevels(vcf)
>> # [1] "chr22"
>>
>> or specify it later:
>>
>> genome(vcf) <- "hg19"
>> seqinfo(vcf)
>> # Seqinfo object with 1 sequence from hg19 genome; no seqlengths:
>> # seqnames seqlengths isCircular genome
>> # chr22 NA NA hg19
>>
>> Hope this helps,
>> H.
>>
>>
>> On 7/29/20 08:30, Robert Castelo wrote:
>>> hi,
>>>
>>> it looks like either VariantAnnotation::readVcf() or something in the
>>> CollapsedVCF class broke in devel with respect to reading and setting
>>> sequence styles:
>>>
>>> library(VariantAnnotation)
>>>
>>> fl <- system.file("extdata", "chr22.vcf.gz",
>>> package="VariantAnnotation")
>>> vcf <- readVcf(fl, "hg19")
>>> seqlevels(vcf)
>>> [1] "22"
>>> seqlevelsStyle(vcf)
>>> [1] "UCSC"
>>> seqlevelsStyle(vcf) <- "UCSC"
>>> seqlevels(vcf)
>>> [1] "22"
>>>
>>> you can find my session information below. let me know if you want me
>>> to open an issue at the GitHub repo (VariantAnnotatoin or
>>> GenomeInfoDb?).
>>>
>>> thanks!
>>>
>>> robert.
>>>
>>> BiocManager::version()
>>> [1] ‘3.12’
>>> 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] VariantAnnotation_1.35.3 Rsamtools_2.5.3
>>> [3] Biostrings_2.57.2 XVector_0.29.3
>>> [5] SummarizedExperiment_1.19.6 DelayedArray_0.15.7
>>> [7] matrixStats_0.56.0 Matrix_1.2-18
>>> [9] Biobase_2.49.0 GenomicRanges_1.41.5
>>> [11] GenomeInfoDb_1.25.8 IRanges_2.23.10
>>> [13] S4Vectors_0.27.12 BiocGenerics_0.35.4
>>> [15] BiocManager_1.30.10
>>>
>>> loaded via a namespace (and not attached):
>>> [1] progress_1.2.2 tidyselect_1.1.0 purrr_0.3.4
>>> [4] lattice_0.20-41 vctrs_0.3.1 generics_0.0.2
>>> [7] BiocFileCache_1.13.0 rtracklayer_1.49.4 GenomicFeatures_1.41.2
>>> [10] blob_1.2.1 XML_3.99-0.4 rlang_0.4.6
>>> [13] pillar_1.4.4 glue_1.4.1 DBI_1.1.0
>>> [16] rappdirs_0.3.1 BiocParallel_1.23.2 bit64_0.9-7.1
>>> [19] dbplyr_1.4.4 GenomeInfoDbData_1.2.3 lifecycle_0.2.0
>>> [22] stringr_1.4.0 zlibbioc_1.35.0 memoise_1.1.0
>>> [25] biomaRt_2.45.2 curl_4.3 AnnotationDbi_1.51.3
>>> [28] Rcpp_1.0.4.6 BSgenome_1.57.5 openssl_1.4.1
>>> [31] bit_1.1-15.2 hms_0.5.3 askpass_1.1
>>> [34] digest_0.6.25 stringi_1.4.6 dplyr_1.0.0
>>> [37] grid_4.0.0 tools_4.0.0 bitops_1.0-6
>>> [40] magrittr_1.5 RCurl_1.98-1.2 RSQLite_2.2.0
>>> [43] tibble_3.0.1 crayon_1.3.4 pkgconfig_2.0.3
>>> [46] ellipsis_0.3.1 prettyunits_1.1.1 assertthat_0.2.1
>>> [49] httr_1.4.1 R6_2.4.1 GenomicAlignments_1.25.3
>>> [52] compiler_4.0.0
>>>
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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 using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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