Question: rtracklayer cannot export empty BED file
0
gravatar for foehn
11 months ago by
foehn60
foehn60 wrote:

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 genomicranges bed • 260 views
ADD COMMENTlink modified 11 months ago by Michael Lawrence11k • written 11 months ago by foehn60
Answer: rtracklayer cannot export empty BED file
0
gravatar for Michael Lawrence
11 months ago by
United States
Michael Lawrence11k wrote:

Thanks, should be fixed inĀ 1.42.1.

ADD COMMENTlink written 11 months ago by Michael Lawrence11k

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 REPLYlink written 11 months ago by foehn60

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

ADD REPLYlink written 11 months ago by Michael Lawrence11k

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 REPLYlink written 11 months ago by foehn60

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.

ADD REPLYlink written 11 months ago by Michael Lawrence11k

OK, got you, thanks.

ADD REPLYlink written 11 months ago by foehn60
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