R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
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sla • 0
@65226e26
Last seen 4 days ago
Denmark

We are using the package 'rtracklayer' to load and manipulate bigwig files as part of a larger script. We need to access bigwig files from an http-server, and we can do this smoothly on MacOS, but we can’t get it to work on Windows machines – while local bigwig files can be imported, the http-accessed files can not.

Any tips?

The following example should be generally accessible:

if (!requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
    BiocManager::install("rtracklayer")
}

library(rtracklayer)

bw = 'http://genome-ftp.mbg.au.dk/public/THJ/Seq2PlotR/examples/tracks/HeLa_3pseq/siGFP_xPAP_in_batch1_plus.bw'

rtracklayer::import.bw(bw)

Which gives the following error message (or similar) on various Windows machines (works on various MacOS computers):

Error in seqinfo(ranges) : UCSC library operation failed

In addition: Warning message:

In seqinfo(ranges) : Invalid argument

mustOpenFd: Can't open http://genome-ftp.mbg.au.dk/public/THJ/Seq2PlotR/examples/tracks/HeLa_3pseq/siGFP_xPAP_in_batch1_plus.bw to read

Importantly, the file can be accessed in other ways from the computer and R(studio):

download.file(bw, "bw1")

trying URL 'http://genome-ftp.mbg.au.dk/public/THJ/Seq2PlotR/examples/tracks/HeLa_3pseq/siGFP_xPAP_in_batch1_plus.bw'

Content type '' length 2469907 bytes (2.4 MB)

downloaded 2.4 MB

SessionInfo from RStudio:

R version 3.5.1 (2018-07-02)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:

[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252

[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C

[5] LC_TIME=English_United Kingdom.1252

attached base packages:

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

other attached packages:

[1] rtracklayer_1.42.2 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1

[6] BiocGenerics_0.28.0

loaded via a namespace (and not attached):

[1] XVector_0.22.0 zlibbioc_1.28.0 GenomicAlignments_1.18.1 BiocParallel_1.16.6

[5] lattice_0.20-41 tools_3.5.1 SummarizedExperiment_1.12.0 grid_3.5.1

[9] Biobase_2.42.0 matrixStats_0.56.0 Matrix_1.2-18 GenomeInfoDbData_1.2.0

[13] BiocManager_1.30.16 bitops_1.0-6 RCurl_1.98-1.2 DelayedArray_0.8.0

[17] compiler_3.5.1 Biostrings_2.50.2 Rsamtools_1.34.1 XML_3.99-0.3

Exactly same problem after upgrading R and rtracklayer:

R version 4.0.3 (2020-10-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19043)>

Matrix products: default

locale:

[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252

[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C

[5] LC_TIME=English_United Kingdom.1252

attached base packages:

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

other attached packages:

[1] rtracklayer_1.49.5 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 IRanges_2.24.1 S4Vectors_0.28.1

[6] BiocGenerics_0.36.1

loaded via a namespace (and not attached):

[1] rstudioapi_0.13 XVector_0.30.0 zlibbioc_1.36.0 GenomicAlignments_1.26.0

[5] BiocParallel_1.24.1 lattice_0.20-45 tools_4.0.3 grid_4.0.3

[9] SummarizedExperiment_1.20.0 Biobase_2.50.0 matrixStats_0.61.0 crayon_1.4.2

[13] Matrix_1.3-4 GenomeInfoDbData_1.2.4 BiocManager_1.30.16 bitops_1.0-7

[17] RCurl_1.98-1.5 DelayedArray_0.16.3 compiler_4.0.3 MatrixGenerics_1.2.1

[21] Biostrings_2.58.0 Rsamtools_2.6.0 XML_3.99-0.8

import.bw rtracklayer Windows http • 251 views
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0
Entering edit mode
@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

From import.bw's man page (?import.bw):

BigWig Import and Export

Description:

 These functions support the import and export of the UCSC BigWig
 format, a compressed, binary form of WIG/BEDGraph with a spatial
 index and precomputed summaries. These functions do not work on
 Windows.

Cheers,

H.

Edit: Although the error message you get could admittedly be more informative. Please report to the rtracklayer maintainers by opening an issue on GitHub here. Thanks!

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0
Entering edit mode

Ooops, I missed that one. Ok, I'll report it on GitHub.

Of note, the functions actually do work on Windows when using local bigwig-files (at least the rtracklayer::import function), and the rtracklayer::import function can access bed-files both locally and from http.

Meanwhile, are there any suggestions for an alternative R package that can rapidly read bigwigs from http? I need to read in the coverage (at nucleotide-resolution) within a specified genomic region. I tried to tweak the megadepth::get_coverage function, but that turns out to be way too slow for this particular job.

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