Entering edit mode
Should I be able to import a gzipped BED file from a URL? I'm unsure if this is user error or a bug in rtracklayer::import()
. Any advice is appreciated:
> suppressPackageStartupMessages(library(rtracklayer)) # Directly import()-ing fails > import(BEDFile("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz")) Error in pushBack(line, con) : can only push back on text-mode connections # Downloading and then importing works > a <- tempdir() > download.file("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz", destfile = file.path(a, "wgEncodeDacMapabilityConsensusExcludable.bed.gz")) trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz' Content type 'application/x-gzip' length 4731 bytes ================================================== downloaded 4731 bytes > import(file.path(a, "wgEncodeDacMapabilityConsensusExcludable.bed.gz")) GRanges object with 411 ranges and 2 metadata columns: seqnames ranges strand | name <Rle> <IRanges> <Rle> | <character> [1] chr1 [ 564450, 570371] * | High_Mappability_island [2] chr1 [ 724137, 727043] * | Satellite_repeat [3] chr1 [ 825007, 825115] * | BSR/Beta [4] chr1 [2583335, 2634374] * | Low_mappability_island [5] chr1 [4363065, 4363242] * | (CATTC)n ... ... ... ... . ... [407] chrY [28555027, 28555353] * | TAR1 [408] chrY [28784130, 28819695] * | Satellite_repeat [409] chrY [58819368, 58917648] * | (CATTC)n [410] chrY [58971914, 58997782] * | (CATTC)n [411] chrY [59361268, 59362785] * | TAR1 score <numeric> [1] 1000 [2] 1000 [3] 1000 [4] 1000 [5] 1000 ... ... [407] 1000 [408] 1000 [409] 1000 [410] 1000 [411] 1000 ------- seqinfo: 25 sequences from an unspecified genome; no seqlengths > sessionInfo() R Under development (unstable) (2016-03-11 r70310) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.3 (El Capitan) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] rtracklayer_1.31.7 GenomicRanges_1.23.24 GenomeInfoDb_1.7.6 [4] IRanges_2.5.40 S4Vectors_0.9.43 BiocGenerics_0.17.3 [7] repete_0.0.0.9002 devtools_1.10.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.3 XVector_0.11.7 [3] magrittr_1.5 zlibbioc_1.17.1 [5] GenomicAlignments_1.7.20 BiocParallel_1.5.20 [7] stringr_1.0.0 tools_3.3.0 [9] SummarizedExperiment_1.1.22 Biobase_2.31.3 [11] digest_0.6.9 pryr_0.1.2 [13] bitops_1.0-6 codetools_0.2-14 [15] RCurl_1.95-4.8 memoise_1.0.0 [17] stringi_1.0-1 Biostrings_2.39.12 [19] Rsamtools_1.23.5 XML_3.98-1.4
Thanks, Michael.
I hacked R to make this work. Hopefully it will get into 3.3 and then this should work after the April/May Bioconductor release.
Cheers, will give it a go then