Hi Valerie, That sounds great! I guess that I would try to keep all the mappings in a single file the next time. The current code grew organically over time, and is not the nicest piece of software I have ever written ☺ Let me take a closer look at this again over the next couple of days, and I may come up with a cleaner, more maintainable solution. Most of this is based on a web page provided by ENSEMBL, and I should be able to come up with a reasonably functional parser for that, assuming that the structure stays more or less the same. They really should provide this information in a proper machine readable form, but hey, it’s ENSEMBL after all… Would you happen to know whether UCSC provides mappings between their genome identifiers and ENSEMBL versions? The only information I could find is here: https://genome.ucsc.edu/FAQ/FAQreleases.html Not quite what we need, even though the assembly name could be parsed and compared with the ENSEMBL genome version string. Florian
we On 26/07/16 21:27, "Obenchain, Valerie" <valerie.obench...@roswellpark.org> wrote: >Hi Florian, > >On 07/21/2016 01:47 AM, Hahne, Florian wrote: >> This is a problem with the biomaRt package and its connection to the Ensembl >> archives, not Gviz. Here’s the call the fails: >> listMarts(host="feb2012.archive.ensembl.org", path="/biomart/martservice") >> >> It looks like Ensembl is no longer providing a download for the feb2012 >> archive. You could try the May2012 one, which according to this table >> (http://www.ensembl.org/info/website/archives/assembly.html) should still >> provide the mm9 (NCBIm37) genome: >> >> bm <- useMart(host = "may2012.archive.ensembl.org", biomart = >> "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl") >> bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643, >> chromosome=7, genome="mm9", biomart = bm) >> >> I’ll update the automated mapping from UCSC genome identifier to Biomart >> within Gviz, however I am more and more convinced that this whole setup is >> not ideal. I simply do not have the time to keep track of all the Ensembl >> changes and new genome versions. There really should be an annotation >> package or the like maintained by Bioconductor core or within the biomaRt >> package that gives a mapping from a UCSC genome identifier to an Ensembl >> genome version and the Ensembl archive to access that. > >The mapping between genome identifiers seems like a natural fit for the >GenomeInfoDb package. Mapping to a particular ensembl archive might be >more appropriate to have in biomaRt but I'm open to what people think. > >If you're in favor of this re-org we can start incorporating the >following into GenomeInfoDb: > >- Gviz:::.getBiobmart() # or move to biomaRt >- Gviz:::.ucsc2Ensembl() >- extdata/biomartVersionsNow.txt >- extdata/biomartVersionsLatest.txt > >Any hints or tips for maintaining the .txt files, i.e., what worked, >what you might do different the second time around? > >Valerie > > > >> >> Florian >> >> >> On 20/07/16 21:15, "Bioc-devel on behalf of James W. MacDonald" >> <bioc-devel-boun...@r-project.org on behalf of jmac...@uw.edu> wrote: >> >>> Hi Holly, >>> >>> This list is intended for those that are developing packages. Your question >>> should be asked on the support site (https://support.bioconductor.org). >>> Please repost over there. >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> On Wed, Jul 20, 2016 at 2:04 PM, Holly <xya...@uchicago.edu> wrote: >>> >>>> Dear Bioconductor helpers, >>>> I am trying to plot a region of interest using the Gviz package. >>>> I met error when running the following example code: >>>>> library(Gviz) >>>>> library(GenomicRanges) >>>>> bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643, >>>> + chromosome=7, genome="mm9") >>>> Entity 'nbsp' not defined >>>> Entity 'hellip' not defined >>>> Entity 'hellip' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'raquo' not defined >>>> Entity 'hellip' not defined >>>> Entity 'hellip' not defined >>>> Entity 'hellip' not defined >>>> Entity 'hellip' not defined >>>> Entity 'hellip' not defined >>>> Opening and ending tag mismatch: img line 68 and li >>>> Opening and ending tag mismatch: li line 68 and ul >>>> Opening and ending tag mismatch: ul line 67 and div >>>> Entity 'copy' not defined >>>> Opening and ending tag mismatch: div line 19 and body >>>> Opening and ending tag mismatch: body line 17 and html >>>> Premature end of data in tag html line 2 >>>> Error: 1: Entity 'nbsp' not defined >>>> 2: Entity 'hellip' not defined >>>> 3: Entity 'hellip' not defined >>>> 4: Entity 'nbsp' not defined >>>> 5: Entity 'raquo' not defined >>>> 6: Entity 'hellip' not defined >>>> 7: Entity 'hellip' not defined >>>> 8: Entity 'hellip' not defined >>>> 9: Entity 'hellip' not defined >>>> 10: Entity 'hellip' not defined >>>> 11: Opening and ending tag mismatch: img line 68 and li >>>> 12: Opening and ending tag mismatch: li line 68 and ul >>>> 13: Opening and ending tag mismatch: ul line 67 and div >>>> 14: Entity 'copy' not defined >>>> 15: Opening and ending tag mismatch: div line 19 and body >>>> 16: Opening and ending tag mismatch: body line 17 and html >>>> 17: Premature end of data in tag html line 2 >>>>> sessionInfo() >>>> R version 3.3.1 (2016-06-21) >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>> Running under: Windows 7 x64 (build 7601) Service Pack 1 >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 >>>> [2] LC_CTYPE=English_United States.1252 >>>> [3] LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C >>>> [5] LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] grid parallel stats4 stats graphics grDevices utils >>>> [8] datasets methods base >>>> >>>> other attached packages: >>>> [1] Gviz_1.16.1 GenomicRanges_1.24.2 GenomeInfoDb_1.8.2 >>>> [4] IRanges_2.6.1 S4Vectors_0.10.2 BiocGenerics_0.18.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] SummarizedExperiment_1.2.3 VariantAnnotation_1.18.3 >>>> [3] splines_3.3.1 lattice_0.20-33 >>>> [5] colorspace_1.2-6 htmltools_0.3.5 >>>> [7] rtracklayer_1.32.1 GenomicFeatures_1.24.4 >>>> [9] chron_2.3-47 interactiveDisplayBase_1.10.3 >>>> [11] survival_2.39-5 XML_3.98-1.4 >>>> [13] foreign_0.8-66 DBI_0.4-1 >>>> [15] ensembldb_1.4.7 BiocParallel_1.6.2 >>>> [17] RColorBrewer_1.1-2 matrixStats_0.50.2 >>>> [19] plyr_1.8.4 zlibbioc_1.18.0 >>>> [21] Biostrings_2.40.2 munsell_0.4.3 >>>> [23] gtable_0.2.0 latticeExtra_0.6-28 >>>> [25] Biobase_2.32.0 biomaRt_2.28.0 >>>> [27] BiocInstaller_1.22.3 httpuv_1.3.3 >>>> [29] AnnotationDbi_1.34.4 Rcpp_0.12.5 >>>> [31] acepack_1.3-3.3 xtable_1.8-2 >>>> [33] BSgenome_1.40.1 scales_0.4.0 >>>> [35] Hmisc_3.17-4 XVector_0.12.0 >>>> [37] mime_0.5 Rsamtools_1.24.0 >>>> [39] gridExtra_2.2.1 AnnotationHub_2.4.2 >>>> [41] ggplot2_2.1.0 digest_0.6.9 >>>> [43] biovizBase_1.20.0 shiny_0.13.2 >>>> [45] tools_3.3.1 bitops_1.0-6 >>>> [47] RCurl_1.95-4.8 RSQLite_1.0.0 >>>> [49] dichromat_2.0-0 Formula_1.2-1 >>>> [51] cluster_2.0.4 Matrix_1.2-6 >>>> [53] data.table_1.9.6 httr_1.2.1 >>>> [55] R6_2.1.2 rpart_4.1-10 >>>> [57] GenomicAlignments_1.8.4 nnet_7.3-12 >>>> Thank you for help, >>>> Holly >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> _______________________________________________ >> Bioc-devel@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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
