Why export of empty GRanges to GFF fails?
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jiri.hon ▴ 10
@jirihon-7904
Last seen 3.2 years ago
Czech Republic

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
rtracklayer • 836 views
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@michael-lawrence-3846
Last seen 2.4 years ago
United States

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

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