Question

rtracklayer cannot export empty BED file

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foehn ▴ 100

@foehn-16281

Last seen 2.6 years ago

United States

Hello,

I found one issue with rtracklayer's export.bed function. It seems that it cannot export an empty GRanges object. For example,

> export(GRanges(), con = "test.bed")
Error in `$<-.data.frame`(`*tmp*`, "score", value = 0) :
  replacement has 1 row, data has 0
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rtracklayer_1.38.3   GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
[4] IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-35            matrixStats_0.54.0        
 [3] XML_3.99-0                 Rsamtools_1.30.0          
 [5] Biostrings_2.46.0          GenomicAlignments_1.14.1  
 [7] bitops_1.0-6               grid_3.4.1                
 [9] zlibbioc_1.24.0            XVector_0.18.0            
[11] Matrix_1.2-14              BiocParallel_1.12.0       
[13] tools_3.4.1                Biobase_2.38.0            
[15] RCurl_1.96-0               DelayedArray_0.4.1        
[17] compiler_3.4.1             SummarizedExperiment_1.8.1
[19] GenomeInfoDbData_0.99.1

Actually, this problem seems to be related to Why export of empty GRanges to GFF fails?, where it was reported that export.gff raised an error upon an empty object.

Can anybody give a look?

Thanks

rtracklayer bed genomicranges • 1.2k views

ADD COMMENT • link updated 5.4 years ago by Michael Lawrence ★ 11k • written 5.4 years ago by foehn ▴ 100

score 0 · Answer 1 · 2018-11-20

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

Thanks, should be fixed in 1.42.1.

ADD COMMENT • link 5.4 years ago Michael Lawrence ★ 11k

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Thanks for prompt reply. The current release version is 1.42.0 and devel version 1.43.0. Does it mean I need to install from the devel channel?

ADD REPLY • link 5.4 years ago foehn ▴ 100

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Please wait a day or so for 1.42.1 to hit the repository.

ADD REPLY • link 5.4 years ago Michael Lawrence ★ 11k

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Just tried out v1.43.0 from bioc v3.9 (devel, which depends on R 3.6). Unfortunately it didn't work...

> export(GRanges(), con = "test.bed")
Error in `$<-.data.frame`(`*tmp*`, score, value = 0) :
  replacement has 1 row, data has 0
> sessionInfo()
R Under development (unstable) (2018-11-18 r75627)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] rtracklayer_1.43.0   GenomicRanges_1.35.1 GenomeInfoDb_1.19.1  IRanges_2.17.1       S4Vectors_0.21.5     BiocGenerics_0.29.1  BiocManager_1.30.4   BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] XVector_0.23.0              zlibbioc_1.29.0             GenomicAlignments_1.19.0    BiocParallel_1.17.1         lattice_0.20-38             tools_3.6.0                
 [7] SummarizedExperiment_1.13.0 grid_3.6.0                  Biobase_2.43.0              matrixStats_0.54.0          Matrix_1.2-15               GenomeInfoDbData_1.2.0     
[13] bitops_1.0-6                RCurl_1.95-4.11             DelayedArray_0.9.0          compiler_3.6.0              Biostrings_2.51.1           Rsamtools_1.35.0           
[19] XML_3.98-1.16

ADD REPLY • link 5.4 years ago foehn ▴ 100

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It's 1.43.1 in devel. If you want to get the fix right now, you'll need to get it out of git.