Hi, On 11-11-09 03:33 AM, Tim Rayner wrote: > Hi Marc, > > Thanks very much for looking into this, and also to Michael for > providing the patch. I've upgraded my GRanges package and the code now > runs with a couple of warnings: > >> txdb.Hs2<- makeTranscriptDbFromBiomart(biomart='ensembl', dataset='hsapiens_gene_ensembl') > Download and preprocess the 'transcripts' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) > Download and preprocess the 'splicings' data frame ... OK > Download and preprocess the 'genes' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > Warning messages: > 1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) > else paste(labels, : > duplicated levels will not be allowed in factors anymore > 2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) > else paste(labels, : > duplicated levels will not be allowed in factors anymore > 3: In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) : > chromosome lengths and circularity flags are not available for this > TranscriptDb object The 2 first warnings + the fact that downloading the chrominfo failed is not looking good. Didn't use to be like that. We'll investigate on our side and report later. Cheers, H. > > So I think the problem is basically fixed. I wonder if perhaps the > issue was caused by truncated data transfers; I observed several > similar failures earlier yesterday afternoon, but in each case the > problem seemed to occur at a different point in the process. > > Thanks again, > > Tim > > On 8 November 2011 20:16, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >> Hi Tim, >> >> There was a small bug last week for this method caused by a decision at >> ensembl to start supporting psuedoautosomal regions, but it was fixed last >> week and should be fixed with the version of GenomicFeatures reported here. >> I just ran your code locally 4 minutes ago and it still works here. The >> only difference I can see is that my GRanges package is one version higher >> than yours (GenomicRanges_1.6.2). Please update that package and then run >> it again and see if you have better luck with ensembl. >> >> The patch that Michael mentioned actually arrived at the exact moment that I >> was testing the bug fix above which means that it has a some conflicts I >> will have to resolve, but it should be added to devel very soon. >> >> >> Marc >> >> >> >> On 11/08/2011 03:55 AM, Michael Lawrence wrote: >>> >>> On Tue, Nov 8, 2011 at 3:19 AM, Tim Rayner<tfrayner at="" gmail.com=""> wrote: >>> >>>> Hi, >>>> >>>> I'm trying to make a TranscriptDb from the Ensembl human Biomart, but >>>> I've run into a problem. As shown below, the equivalent operation for >>>> the mouse Biomart works fine: >>>> >>>>> # Mouse TranscriptDb created without a hitch: >>>>> txdb.Mm<- makeTranscriptDbFromBiomart(biomart='ensembl', >>>> >>>> dataset='mmusculus_gene_ensembl') >>>> Download and preprocess the 'transcripts' data frame ... OK >>>> Download and preprocess the 'chrominfo' data frame ... OK >>>> Download and preprocess the 'splicings' data frame ... OK >>>> Download and preprocess the 'genes' data frame ... OK >>>> Prepare the 'metadata' data frame ... OK >>>> Make the TranscriptDb object ... OK >>>> >>>>> # Here's the problem: >>>>> txdb.Hs<- makeTranscriptDbFromBiomart(biomart='ensembl', >>>> >>>> dataset='hsapiens_gene_ensembl') >>>> Download and preprocess the 'transcripts' data frame ... OK >>>> Download and preprocess the 'chrominfo' data frame ... FAILED! (=> >>>> skipped) >>>> Download and preprocess the 'splicings' data frame ... Error in >>>> scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : >>>> line 800380 did not have 11 elements >>>> >>>>> sessionInfo() >>>> >>>> R version 2.14.0 (2011-10-31) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] GenomicFeatures_1.6.1 AnnotationDbi_1.16.0 Biobase_2.14.0 >>>> [4] GenomicRanges_1.6.1 IRanges_1.12.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 >>>> RCurl_1.6-10 >>>> [5] RSQLite_0.10.0 XML_3.4-3 biomaRt_2.10.0 >>>> rtracklayer_1.14.1 >>>> [9] tools_2.14.0 zlibbioc_1.0.0 >>>> >>>> I don't know if this is an issue with the Biomart instance or the >>>> GenomicFeatures package. I was wondering if anyone had any suggestions >>>> as to how I might work around this? >>>> >>>> On a related note, would it be possible to add the ability to point >>>> makeTranscriptDbFromBiomart() at alternate Biomart hosts (as one >>>> would, for example, by calling >>>> biomaRt::useMart(host='www.ensembl.org', ...))? >>> >>> We've submitted a patch that does just this, as well as supporting an >>> attribute prefix string for selecting alternative gene models. >>> >>> >>>> It would probably be >>>> good to be able to pass through the 'archive' argument to useMart as >>>> well. >>>> >>>> Many thanks, >>>> >>>> Tim Rayner >>>> >>>> -- >>>> Bioinformatician >>>> Smith Lab, CIMR >>>> University of Cambridge >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. 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