Import Chain - Cannot Import Chain File
1
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kipperf • 0
@kipperf-16916
Last seen 4.1 years ago

Hi,

I am trying to use rtracklayer's import.chain function to load a chain file from UCSC. However, I get a weird error. Below is a reproducible example and the error I get. What is happening here?

library(rtracklayer)

download.file("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/vsSelf/hg19.hg19.all.chain.gz",
              "hg19.hg19.all.chain.gz")

system("gzip -d hg19.hg19.all.chain.gz")

chain <- import.chain("hg19.hg19.all.chain")

The error is:

Error in .local(con, format, text, ...) : expected 11 elements in header, got 3, on line 1

What is import looking for here? My sessionInfo() is below.


R version 3.3.0 (2016-05-03) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

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] rtracklayer_1.32.2 AnnotationHub_2.4.2 [3] InteractionSet_1.0.4 SummarizedExperiment_1.2.3 [5] Biobase_2.32.0 GenomicRanges_1.24.3 [7] GenomeInfoDb_1.8.7 IRanges_2.6.1 [9] S4Vectors_0.10.3 BiocGenerics_0.18.0 [11] Chicago_1.0.4 data.table_1.10.4-3 [13] magrittr_1.5 scales_0.5.0.9000

loaded via a namespace (and not attached): [1] Rcpp_0.12.14 lattice_0.20-33 [3] Delaporte_6.2.0 Rsamtools_1.24.0 [5] Biostrings_2.40.2 digest_0.6.12 [7] mime_0.5 R6_2.2.2 [9] plyr_1.8.4 backports_1.1.2 [11] acepack_1.4.1 RSQLite_1.0.0 [13] httr_1.3.1 ggplot2_2.2.1.9000 [15] BiocInstaller_1.22.3 zlibbioc_1.18.0 [17] rlang_0.1.4 lazyeval_0.2.1 [19] curl_3.0 rstudioapi_0.6 [21] rpart_4.1-10 Matrix_1.2-6 [23] checkmate_1.8.5 splines_3.3.0 [25] BiocParallel_1.6.6 stringr_1.2.0 [27] foreign_0.8-66 htmlwidgets_0.9 [29] RCurl_1.95-4.8 munsell_0.4.3 [31] shiny_1.0.3 compiler_3.3.0 [33] httpuv_1.3.5 base64enc_0.1-3 [35] htmltools_0.3.6 nnet_7.3-12 [37] tibble_1.3.4 gridExtra_2.3 [39] htmlTable_1.12 interactiveDisplayBase_1.10.3 [41] Hmisc_4.1-1 matrixStats_0.54.0 [43] XML_3.98-1.4 GenomicAlignments_1.8.4 [45] bitops_1.0-6 MASS_7.3-45 [47] grid_3.3.0 xtable_1.8-2 [49] gtable_0.2.0 DBI_0.5 [51] stringi_1.1.6 XVector_0.12.1 [53] latticeExtra_0.6-28 Formula_1.2-3 [55] RColorBrewer_1.1-2 tools_3.3.0 [57] survival_2.42-6 AnnotationDbi_1.34.4 [59] colorspace_1.2-6 cluster_2.0.4 [61] knitr_1.14
rtracklayer • 1.4k views
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1
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@michael-lawrence-3846
Last seen 10 months ago
United States

Looks like the UCSC chain file format has changed, or at least they are using features that they weren't before. It may take a bit for me to fix the parser.

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0
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Ok version 1.40.5 (release) should have the fix. We needed to ignore comments (apparently an undocumented feature of the format).

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Thanks for the quick turnaround!

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0
Entering edit mode

It seems that the problem is back with import.chain(), despite rtracklayer_1.50.0. Is that (https://genome.ucsc.edu/goldenPath/help/chain.html) still the expected format?

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