[Bioc-devel] BiomartGeneRegionTrack question

Hahne, Florian florian.hahne at novartis.com
Wed Jul 27 10:18:32 CEST 2016 

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.Obenchain at 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-bounces at r-project.org on behalf of jmacdon at 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 <xyang2 at 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")
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>>>> Entity 'raquo' not defined
>>>> Entity 'hellip' not defined
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>>>> 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 at 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 at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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