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.conductor/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
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>



-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

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