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Question: Why export of empty GRanges to GFF fails?
0
gravatar for jiri.hon
16 months ago by
jiri.hon0
Czech Republic
jiri.hon0 wrote:

An attempt to export an empty GRanges object to GFF using export function from rtracklayer package fails. Is this behavior intended or is it a bug?

> library(rtracklayer)
> export(GRanges(), "test.gff", version = "3")
Error in data.frame(seqname, source, feature, start(object), end(object),  : 
  arguments imply differing number of rows: 0, 1
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=cs_CZ.UTF-8       LC_NUMERIC=C               LC_TIME=cs_CZ.UTF-8        LC_COLLATE=cs_CZ.UTF-8    
 [5] LC_MONETARY=cs_CZ.UTF-8    LC_MESSAGES=cs_CZ.UTF-8    LC_PAPER=cs_CZ.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rtracklayer_1.34.2   GenomicRanges_1.26.3 GenomeInfoDb_1.10.3  IRanges_2.8.1        S4Vectors_0.12.1    
[6] BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] lattice_0.20-34            XML_3.98-1.5               Rsamtools_1.26.1           Biostrings_2.42.1         
 [5] bitops_1.0-6               GenomicAlignments_1.10.0   grid_3.3.2                 zlibbioc_1.20.0           
 [9] XVector_0.14.0             Matrix_1.2-8               BiocParallel_1.8.1         tools_3.3.2               
[13] Biobase_2.34.0             RCurl_1.95-4.8             SummarizedExperiment_1.4.0
ADD COMMENTlink modified 15 months ago by Michael Lawrence10.0k • written 16 months ago by jiri.hon0
2
gravatar for Michael Lawrence
15 months ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

Thanks, this should be fixed in version 1.35.7 (devel).

ADD COMMENTlink written 15 months ago by Michael Lawrence10.0k
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