Hi Malcolm, It's fixed in released branch, 1.10.3, please update and try two days later, the bug you reported is not quite related to CDS parsing, but a bug around how biovizBase handle the empty object exception. Thanks Tengfei On Mon, Nov 4, 2013 at 5:02 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Malcolm, > > Thanks for reporting the issue and provide the attached example, I am > looking into this and will keep you updated. > > cheers > > Tengfei > > > On Mon, Nov 4, 2013 at 11:36 AM, Cook, Malcolm <mec@stowers.org> wrote: > >> Tengfei & Herve, >> >> I too am afflicted with this error and hoping that the following >> reproducible example will hasten a patch. >> >> I am unsure but speculate that this error is raised for the same >> transcripts wherein makeTranscriptDbFromUCSC issues warning: >> In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) : >> UCSC data anomaly in 434 transcript(s): the cds cumulative length is >> not a multiple of 3 for transcripts 'HRA1' 'tP(UGG)A' 'snR18' 'tA(UGC)A' >> 'tL(CAA)A' 'tS(AGA)A' 'YAR061W' 'YAR062W' 'tP(UGG)Q' '15S_rRNA' 'tW(UCA)Q' >> 'tE(UUC)Q' 'tS(UGA)Q2' '21S_rRNA' 'tT(UGU)Q1' 'tC(GCA)Q' 'tH(GUG)Q' >> 'tL(UAA)Q' 'tQ(UUG)Q' 'tK(UUU)Q' 'tR(UCU)Q1' 'tG(UCC)Q' 'tD(GUC)Q' >> 'tS(GCU)Q1' 'tR(ACG)Q2' 'tA(UGC)Q' 'tI(GAU)Q' 'tY(GUA)Q' 'tN(GUU)Q' >> 'tM(CAU)Q1' 'tF(GAA)Q' 'tT(XXX)Q2' 'tV(UAC)Q' 'tM(CAU)Q2' 'RPM1' 'snR80' >> 'snR67' 'snR53' 'tG(GCC)E' 'tS(AGA)E' >> 'tM(CAU)E' 'RPR1' 'tQ(UUG)E2' 'tK(CUU)E1' 'tR(UCU)E' 'snR14' >> 'tE(UUC)E1' 'tH(GUG)E1' 'tQ(UUG)E1' 'tS(UGA)E' 'tA(UGC)E' 'SRG1' >> 'tE(UUC)E2' 'snR4' 'snR52' 'tH(GUG)E2' 'tK(CUU)E2' 'tV(AAC)E1' 'SCR1' >> 'tI(AAU)E1' 'tV(AAC)E2' ' [... truncated] >> >> Regarding which, the following thread may be of interest: >> https://stat.ethz.ch/pipermail/bioconductor/2010-July/034568.html >> https://stat.ethz.ch/pipermail/bioconductor/2012-March/044214.html >> >> http://permalink.gmane.org/gmane.science.biology.informatics.conduc tor/30105 >> >> In the last thread, Herve, you wonder: >> > Should we allow >> > the user to filter CDSs based on this status? Or should we import only >> > complete CDSs? Or we import all the CDSs but we store in the metadata >> > table of the TranscriptDb object (and then display this in the show >> > method) the fact that not all the CDSs are complete? >> >> In my case, a great workaround would be to provide option the drop (with >> warning) the incomplete ones. Or, somehow interrogate the tr.db for which >> have this problem so I may drop them myself. >> >> Tengfie, It would be great if any fix that works in the development >> version can be ported to the release branch as well. >> >> Cheers, >> >> ~Thanks, >> >> Malcolm >> >> library(ggbio) >> library(GenomicFeatures) >> >> tr.db<- >> makeTranscriptDbFromUCSC( >> ,genome='sacCer3' >> ,tablename='ensGene' >> ) >> >> tr.by.gn.grl<-transcriptsBy(tr.db,'gene') >> >> gn.gr<-unlist(range(tr.by.gn.grl),use.names=TRUE) >> >> a2<-geom_alignment(tr.db,which=gn.gr[2]) # this works! >> >> geom_alignment(tr.db,which=gn.gr['HRA1']) # this breaks >> >> >> gn.gr[1] >> sessionInfo() >> >> >> ## whose output is: >> >> >> In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) : >> UCSC data anomaly in 434 transcript(s): the cds cumulative length is >> not a multiple of 3 for transcripts 'HRA1' 'tP(UGG)A' 'snR18' 'tA(UGC)A' >> 'tL(CAA)A' 'tS(AGA)A' 'YAR061W' 'YAR062W' 'tP(UGG)Q' '15S_rRNA' 'tW(UCA)Q' >> 'tE(UUC)Q' 'tS(UGA)Q2' '21S_rRNA' 'tT(UGU)Q1' 'tC(GCA)Q' 'tH(GUG)Q' >> 'tL(UAA)Q' 'tQ(UUG)Q' 'tK(UUU)Q' 'tR(UCU)Q1' 'tG(UCC)Q' 'tD(GUC)Q' >> 'tS(GCU)Q1' 'tR(ACG)Q2' 'tA(UGC)Q' 'tI(GAU)Q' 'tY(GUA)Q' 'tN(GUU)Q' >> 'tM(CAU)Q1' 'tF(GAA)Q' 'tT(XXX)Q2' 'tV(UAC)Q' 'tM(CAU)Q2' 'RPM1' 'snR80' >> 'snR67' 'snR53' 'tG(GCC)E' 'tS(AGA)E' >> 'tM(CAU)E' 'RPR1' 'tQ(UUG)E2' 'tK(CUU)E1' 'tR(UCU)E' 'snR14' >> 'tE(UUC)E1' 'tH(GUG)E1' 'tQ(UUG)E1' 'tS(UGA)E' 'tA(UGC)E' 'SRG1' >> 'tE(UUC)E2' 'snR4' 'snR52' 'tH(GUG)E2' 'tK(CUU)E2' 'tV(AAC)E1' 'SCR1' >> 'tI(AAU)E1' 'tV(AAC)E2' ' [... truncated] >> >> Aggregating TranscriptDb... >> Parsing exons... >> Parsing cds... >> Parsing transcripts... >> Parsing utrs and aggregating... >> Done >> Constructing graphics... >> > > >> Aggregating TranscriptDb... >> Parsing exons... >> Parsing cds... >> Parsing transcripts... >> Parsing utrs and aggregating... >> Error in data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, >> : >> arguments imply differing number of rows: 0, 1 >> > > > >> GRanges with 1 range and 0 metadata columns: >> seqnames ranges strand >> <rle> <iranges> <rle> >> 15S_rRNA chrM [6546, 8194] + >> --- >> seqlengths: >> chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII >> chrIX chrX chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM >> 230218 813184 316620 1531933 576874 270161 1090940 562643 >> 439888 745751 666816 1078177 924431 784333 1091291 948066 85779 >> > >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 >> LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices datasets utils methods >> base >> >> other attached packages: >> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.4 >> BiocGenerics_0.8.0 ggbio_1.10.0 ggplot2_0.9.3.1 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.0 biovizBase_1.10.0 >> bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >> colorspace_1.2-4 compiler_3.0.2 DBI_0.2-7 >> dichromat_2.0-0 digest_0.6.3 grid_3.0.2 >> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >> labeling_0.2 lattice_0.20-24 MASS_7.3-29 >> munsell_0.4.2 plyr_1.8 proto_0.3-10 >> RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 >> [25] rpart_4.1-3 Rsamtools_1.14.1 RSQLite_0.11.4 >> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >> stringr_0.6.2 tools_3.0.2 VariantAnnotation_1.8.2 >> XML_3.98-1.1 zlibbioc_1.8.0 >> > >> >> >-----Original Message----- >> >From: bioconductor-bounces@r-project.org [mailto: >> bioconductor-bounces@r-project.org] On Behalf Of Tengfei Yin >> >Sent: Friday, October 18, 2013 12:05 PM >> >To: Alejandro Reyes >> >Cc: bioconductor@r-project.org >> >Subject: Re: [BioC] autoplot transcriptDb error with some regions >> > >> >Hi Alejandro, >> > >> >Thanks for reporting, I believe that's a bug caused by my recent >> >modification in biovizBase package, I am working on that now, will keep >> you >> >updated. >> > >> >Best >> > >> >Tengfei >> > >> > >> >On Fri, Oct 18, 2013 at 12:43 PM, Alejandro Reyes >> ><alejandro.reyes@embl.de>wrote: >> > >> >> Dear Tengfei Yin, >> >> >> >> Firstly, thanks for developing ggbio, it has been very useful for me! >> >> >> >> I am getting an error when using autoplot with some specific genomic >> >> regions in transcriptDb objects, here is an example: >> >> >> >> > suppressMessages( library(ggbio) ) >> >> > suppressMessages(library(**GenomicFeatures)) >> >> > tx <- makeTranscriptDbFromBiomart() >> >> >> >> Aggregating TranscriptDb... >> >> Parsing exons... >> >> Parsing cds... >> >> Parsing transcripts... >> >> Parsing utrs and aggregating... >> >> Done >> >> Constructing graphics... >> >> >> >> prueba <- GRanges( 16, IRanges( start=69598997, 69718569 ) ) >> >> autoplot( tx, prueba, group.selfish=TRUE, names.expr="") >> >> >> >> Aggregating TranscriptDb... >> >> Parsing exons... >> >> Parsing cds... >> >> Parsing transcripts... >> >> Parsing utrs and aggregating... >> >> Done >> >> Constructing graphics... >> >> >> >> So far, excellent, however, when I look into a smaller region I get an >> >> error message: >> >> >> >> > prueba <- GRanges( "16", IRanges(start=69718724, end=69720078 )) >> >> > autoplot( tx, prueba, group.selfish=TRUE, names.expr="") >> >> Aggregating TranscriptDb... >> >> Parsing exons... >> >> Parsing cds... >> >> Parsing transcripts... >> >> Parsing utrs and aggregating... >> >> Error in DataFrame(...) : different row counts implied by arguments >> >> >> >> I believe it has to do with recent modifications of ggbio, since I do >> not >> >> get the error message with older versions, e.g. 1.9.7. >> >> >> >> > sessionInfo() >> >> R Under development (unstable) (2013-07-01 r63121) >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> >> >> 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=en_US.UTF-8 >> >> [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] parallel stats graphics grDevices utils datasets methods >> >> [8] base >> >> >> >> other attached packages: >> >> [1] ggbio_1.11.0 ggplot2_0.9.3.1 GenomicFeatures_1.15.0 >> >> [4] AnnotationDbi_1.23.28 Biobase_2.21.7 GenomicRanges_1.13.56 >> >> [7] XVector_0.1.4 IRanges_1.19.40 BiocGenerics_0.7.8 >> >> [10] BiocInstaller_1.13.1 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] biomaRt_2.17.3 Biostrings_2.29.19 biovizBase_1.9.4 >> >> [4] bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4 >> >> [7] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> >> [10] digest_0.6.3 grid_3.1.0 gridExtra_0.9.1 >> >> [13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2 >> >> [16] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >> >> [19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >> >> [22] RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >> >> [25] Rsamtools_1.13.53 RSQLite_0.11.4 rtracklayer_1.21.14 >> >> [28] scales_0.2.3 stats4_3.1.0 stringr_0.6.2 >> >> [31] tools_3.1.0 VariantAnnotation_1.7.57 XML_3.98-1.1 >> >> [34] zlibbioc_1.7.0 >> >> >> >> Best regards, >> >> Alejandro Reyes >> >> >> > >> > >> > >> >-- >> >Tengfei Yin, PhD >> >Seven Bridges Genomics >> >sbgenomics.com >> >625 Mt. Auburn St. Suite #208 >> >Cambridge, MA 02138 >> >(617) 866-0446 >> > >> > [[alternative HTML version deleted]] >> > >> >_______________________________________________ >> >Bioconductor mailing list >> >Bioconductor@r-project.org >> >https://stat.ethz.ch/mailman/listinfo/bioconductor >> >Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]