[Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

[Cook, Malcolm]

.Hi Tengfei,
 .
 .Yes that looks like an oversight.  Thanks for reporting that!  I will
 .extend makeTxDbPackage so that it's more accommodating of these newer
 .transcriptDbs.  If you want to help me out, you could call saveDb() on
 .your gmax189 object and send me the .sqlite file that you save it to.
 .
 .Also, if you have any alternate options for importing your data (other
 .than using GFF or GTF): I think you probably should consider it.  The
 .file specifications for these filetypes are missing key details and so
 .you can very easily get a "legal" GFF or GTF file that is actually
 .missing important details from it's contents.  For example, they can
 .commonly lack information about the order of the exons for a given
 .transcript, which can render them difficult (or impossible) to use for
 .transcript work.   But for these specifications, that information is
 ."optional".

Marco, do you have any comment on ensembl GTF (which has exon order) in this regard?

Thanks,

Malcolm

 .
 .
 .   Marc
 .
 .
 .
 .On 02/06/2013 09:46 PM, Tengfei Yin wrote:
 .> Dear all,
 .>
 .> I am trying to build a txdb object from gff3 for soybean data and try to
 .> make it a package. Code used like this
 .>
 .> gmax189<- makeTranscriptDbFromGFF("~/Gmax_189_gene_exons.gff3",
 .>                                     format = "gff3", species = "Glycine max",
 .>                                     dataSource = "http://www.phytozome.org/")
 .> makeTxDbPackage(txdb = gmax189,
 .>                  version = "0.9.1",
 .>                  maintainer = "Tengfei Yin",
 .>                  author = "Tengfei Yin",
 .>                  destDir=".",
 .>                  license="Artistic-2.0")
 .>
 .> Error message:
 .> Error in gsub("_", "", pkgName) :
 .>    error in evaluating the argument 'x' in selecting a method for function
 .> 'gsub': Error: object 'pkgName' not found
 .>
 .>
 .> Looks like my dataSource should be either BioMart or UCSC, otherwise no
 .> pkgname will be produced in function .makePackageName?
 .>
 .> Or should I build annotation package in some other ways?
 .>
 .> Thanks a lot
 .>
 .> Tengfei
 .>
 .> my sessionInfo
 .>
 .>> sessionInfo()
 .> R Under development (unstable) (2013-01-21 r61728)
 .> 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=C                 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] GenomicFeatures_1.11.8 AnnotationDbi_1.21.10  Biobase_2.19.2
 .> [4] GenomicRanges_1.11.28  IRanges_1.17.31        BiocGenerics_0.5.6
 .>
 .> loaded via a namespace (and not attached):
 .>   [1] biomaRt_2.15.0     Biostrings_2.27.10 bitops_1.0-5
 .> BSgenome_1.27.1
 .>   [5] DBI_0.2-5          RCurl_1.95-3       Rsamtools_1.11.15
 .>   RSQLite_0.11.2
 .>   [9] rtracklayer_1.19.9 stats4_3.0.0       tools_3.0.0        XML_3.95-0.1
 .>
 .> [13] zlibbioc_1.5.0
 .>
 .>
 .
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