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Question: Gviz UcscTrack error
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3.9 years ago by
Guest User12k
Guest User12k wrote:
Dear All, Gviz refuses to generate a UcscTrack. The code below worked in the middle of December: genetrack=UcscTrack(track="RefSeq Genes", table="refGene", trackType="GeneRegionTrack",chromosome="chr5", genome="mm9", rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", transcript="name", strand="strand", name="RefSeq Genes", feature="name2", showId=T, from=30334169, to=30349988, fill = "green") But now it generates the following error: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 2 elements R as well as Bioconductor version is up-to-date. Does anyone know what the problem might be? Thanks a lot! Ania -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 [6] Gviz_1.6.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0 Biostrings_2.30.1 [5] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 [9] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 Formula_1.1-1 [13] GenomicFeatures_1.14.2 Hmisc_3.13-0 labeling_0.2 lattice_0.20-24 [17] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 [21] RCurl_1.95-4.1 Rsamtools_1.14.2 RSQLite_0.11.4 scales_0.2.3 [25] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-4 [29] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 3.9 years ago by florian.hahne@novartis.com1.5k • written 3.9 years ago by Guest User12k
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3.9 years ago by
Switzerland
Hi Ania, I can't seem to reproduce your problem here: > library(Gviz) Loading required package: grid > genetrack=UcscTrack(track="RefSeq Genes", table="refGene", + trackType="GeneRegionTrack",chromosome="chr5", genome="mm9", + rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", + transcript="name", strand="strand", name="RefSeq Genes", feature="name2", + showId=T, from=30334169, to=30349988, fill = "green") > sessionInfo() R version 3.0.2 Patched (2013-10-27 r64116) Platform: i386-apple-darwin12.5.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 Biobase_2.22.0 [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 [7] BiocGenerics_0.8.0 Gviz_1.6.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.7 [4] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 [7] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 [10] Formula_1.1-1 Hmisc_3.13-0 labeling_0.2 [13] lattice_0.20-24 latticeExtra_0.6-26 munsell_0.4.2 [16] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 [19] Rsamtools_1.14.2 RSQLite_0.11.4 rtracklayer_1.22.0 [22] scales_0.2.3 splines_3.0.2 stats4_3.0.2 [25] stringr_0.6.2 survival_2.37-4 tools_3.0.2 [28] XML_3.98-1.1 zlibbioc_1.8.0 Maybe the UCSC server had some issue on the day you tried this? Could you please check again today whether the problem has gone away? Both Gviz and rtracklayer versions are the same on my machine and yours, so package versions should not be an issue. The only difference I see in the sessionInfo is a slightly newer R version in my end (3.0.2 Patched) If all that you are interested in are RefSeq gene models from UCSC you might as well consider building a GeneRegionTrack directly from a TranscriptDB object. This should be much more efficient and you will also get UTR information for free. Please see the package vignette for details. Florian On 1/7/14 10:44 PM, "Anna Sawicka [guest]" <guest at="" bioconductor.org=""> wrote: >genetrack=UcscTrack(track="RefSeq Genes", table="refGene", > trackType="GeneRegionTrack",chromosome="chr5", >genome="mm9", > rstart="exonStarts", rends="exonEnds", gene="name", >symbol="name2", > transcript="name", strand="strand", name="RefSeq >Genes", feature="name2", > showId=T, from=30334169, to=30349988, fill = "green")
ADD COMMENTlink written 3.9 years ago by florian.hahne@novartis.com1.5k
Dear Florian, thank you for the response. Everything works today. This must have been a server problem. And thanks a lot for you suggestion concerning RefSeq gene models! Best wishes, Ania > Hi Ania, > I can't seem to reproduce your problem here: >> library(Gviz) > Loading required package: grid >> genetrack=UcscTrack(track="RefSeq Genes", table="refGene", > > + trackType="GeneRegionTrack",chromosome="chr5", > genome="mm9", > + rstart="exonStarts", rends="exonEnds", gene="name", > symbol="name2", > + transcript="name", strand="strand", name="RefSeq > Genes", feature="name2", > + showId=T, from=30334169, to=30349988, fill = "green") >> sessionInfo() > R version 3.0.2 Patched (2013-10-27 r64116) > Platform: i386-apple-darwin12.5.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 Biobase_2.22.0 > [4] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 > [7] BiocGenerics_0.8.0 Gviz_1.6.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.7 > [4] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 > [7] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 > [10] Formula_1.1-1 Hmisc_3.13-0 labeling_0.2 > [13] lattice_0.20-24 latticeExtra_0.6-26 munsell_0.4.2 > [16] plyr_1.8 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [19] Rsamtools_1.14.2 RSQLite_0.11.4 rtracklayer_1.22.0 > [22] scales_0.2.3 splines_3.0.2 stats4_3.0.2 > [25] stringr_0.6.2 survival_2.37-4 tools_3.0.2 > [28] XML_3.98-1.1 zlibbioc_1.8.0 > > Maybe the UCSC server had some issue on the day you tried this? Could you > please check again today whether the problem has gone away? Both Gviz and > rtracklayer versions are the same on my machine and yours, so package > versions should not be an issue. The only difference I see in the > sessionInfo is a slightly newer R version in my end (3.0.2 Patched) > > If all that you are interested in are RefSeq gene models from UCSC you > might as well consider building a GeneRegionTrack directly from a > TranscriptDB object. This should be much more efficient and you will also > get UTR information for free. Please see the package vignette for details. > > Florian > > > > > > > On 1/7/14 10:44 PM, "Anna Sawicka [guest]" <guest at="" bioconductor.org=""> wrote: > >> genetrack=UcscTrack(track="RefSeq Genes", table="refGene", >> trackType="GeneRegionTrack",chromosome="chr5", >> genome="mm9", >> rstart="exonStarts", rends="exonEnds", gene="name", >> symbol="name2", >> transcript="name", strand="strand", name="RefSeq >> Genes", feature="name2", >> showId=T, from=30334169, to=30349988, fill = "green") >
ADD REPLYlink written 3.9 years ago by Anna Sawicka20
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