[Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

[Michael Lawrence]

I'm curious as to why you are looping over the views in the first
place. Maybe we could arrive at a vectorized solution, which is often
but not always simpler and faster.

Michael

On Wed, Apr 5, 2017 at 8:13 PM, Pariksheet Nanda
<pariksheet.nanda at uconn.edu> wrote:
> Hi bioconductor devs,
>
> The BSgenomeViews class has been very useful in efficiently propagating
> metadata for running Biostring operations.  I noticed something unexpected
> when iterating over views - it seems to return the Biostrings object
> instead of a single length Views object, and thus loses the associated view
> metadata.  Is this intentional?  Below is some example code, the output and
> sessionInfo().  Yes, I also confirmed this happens in the development
> version of R / bioconductor 3.5.
>
> On a side note, for unit testing it's been difficult to mock a BSgenome
> object due to the link to physical files, and as a workaround I use a
> small, arbitrary BSgenome package.  Can one construct a BSgenome from its
> package bundled extdata?  The man page examples use packaged genomes.
>
> Code to reproduce the issue:
>
> ----------------------------------------------------------------------
> library(BSgenome)
> genome <- getBSgenome("BSgenome.Hsapiens.UCSC.hg19")
> gr <- GRanges(c("chr1:25001-28000", "chr2:30001-31000"))
> views <- Views(genome, gr)
> views
> lapply(views, class)
> ----------------------------------------------------------------------
>
> Result:
>
> ----------------------------------------------------------------------
>> views
> BSgenomeViews object with 2 views and 0 metadata columns:
>       seqnames         ranges strand                       dna
>          <Rle>      <IRanges>  <Rle>            <DNAStringSet>
>   [1]     chr1 [25001, 28000]      * [GCTTCAGCCT...TTATTTATTG]
>   [2]     chr2 [30001, 31000]      * [GACCCTCCTG...AGCAGGTGGT]
>   -------
>   seqinfo: 93 sequences (1 circular) from hg19 genome
>> lapply(views, class)
> [[1]]
> [1] "DNAString"
> attr(,"package")
> [1] "Biostrings"
>
> [[2]]
> [1] "DNAString"
> attr(,"package")
> [1] "Biostrings"
>
>>
> ----------------------------------------------------------------------
>
> Tested against these configurations:
> 1) R 3.3.2 + BSgenome 1.42.0 (stable bioconductor 3.4)
> 2) R 2017-04-05 installed via llnl/spack + BSgenome 1.43.7 (devel
> bioconductor 3.5)
>
> sessionInfo for configuration #2 above:
> ----------------------------------------------------------------------
>> sessionInfo()
> R Under development (unstable) (2017-04-05 r72488)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.2 LTS
>
> Matrix products: default
> BLAS:
> /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-04-05-4tkzhsu6sdpwmlvnv275jf6x766gwnpy/rlib/R/lib/libRblas.so
> LAPACK:
> /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-04-05-4tkzhsu6sdpwmlvnv275jf6x766gwnpy/rlib/R/lib/libRlapack.so
>
> 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=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.43.7
>  [3] rtracklayer_1.35.10               Biostrings_2.43.7
>  [5] XVector_0.15.2                    GenomicRanges_1.27.23
>  [7] GenomeInfoDb_1.11.10              IRanges_2.9.19
>  [9] S4Vectors_0.13.15                 BiocGenerics_0.21.3
>
> loaded via a namespace (and not attached):
>  [1] zlibbioc_1.21.0            GenomicAlignments_1.11.12
>  [3] BiocParallel_1.9.5         lattice_0.20-35
>  [5] tools_3.5.0                SummarizedExperiment_1.5.7
>  [7] grid_3.5.0                 Biobase_2.35.1
>  [9] matrixStats_0.52.1         Matrix_1.2-9
> [11] GenomeInfoDbData_0.99.0    bitops_1.0-6
> [13] RCurl_1.95-4.8             DelayedArray_0.1.7
> [15] compiler_3.5.0             Rsamtools_1.27.15
> [17] XML_3.98-1.6
>> BiocInstaller::biocValid()
> [1] TRUE
>>
>
> ---
> Pariksheet Nanda
> PhD Candidate in Genetics and Genomics
> System Administrator, Storrs HPC Cluster
> University of Connecticut
>
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>
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