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cbaribault
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@cbaribault-12277
Last seen 7.7 years ago
According to the doc for the trackLine parameter...
For import, an imported track line will be stored in a TrackLine object, as part of the returned UCSCData.
Separate but related to rtracklayer bed import, in the code below, the resulting bed file, test.bed, has only a single track line preceding the tabular data. I can load said bed file successfully into the UCSC browser, but the error message during import via rtracklayer is similar to that of said issue. Please see R response and session info further below.
BED_TEXT <- "track name=\"My track\" description=\"My description\" visibility=2 itemRgb=\"On\"
chr1 567890 567899 DAT:0.1234 0 . 0 0 255,0,0"
BED_FILE <- "test.bed"
writeLines(text = BED_TEXT, con = BED_FILE)
tryCatch(
import.bed(BED_FILE),
error = function(e) e, finally = print("Hello 1")
)
tryCatch(
import(con = BED_FILE, format = "bed", trackLine = TRUE, genome = "hg19", extraCols = "character"),
error = function(e) e, finally = print("Hello 2")
)
And the R response for the above...
> BED_TEXT <- "track name=\"My track\" description=\"My description\" visibility=2 itemRgb=\"On\"
+ chr1 567890 567899 DAT:0.1234 0 . 0 0 255,0,0"
> BED_FILE <- "test.bed"
> writeLines(text = BED_TEXT, con = BED_FILE)
> tryCatch(
+ import.bed(BED_FILE), #fails
+ error = function(e) e, finally = print("Hello 1")
+ )
[1] "Hello 1"
<simpleError in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul): line 1 did not have 9 elements>
> tryCatch(
+ import(con = BED_FILE, format = "bed", trackLine = TRUE, genome = "hg19", extraCols = "character"),
+ error = function(e) e, finally .... [TRUNCATED]
[1] "Hello 2"
<simpleError in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul): line 1 did not have 8 elements>
And here's my session info...
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] genomation_1.11.3 goldmine_1.0 rtracklayer_1.38.3 GenomicRanges_1.30.1 GenomeInfoDb_1.14.0 [6] IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 stringi_1.1.6 stringr_1.2.0 [11] gridExtra_2.3 ggplot2_2.2.1 Rcpp_0.12.15 data.table_1.10.4-3 devtools_1.13.4 [16] BiocInstaller_1.28.0 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.8.1 reshape2_1.4.3 lattice_0.20-35 seqPattern_1.10.0 [5] colorspace_1.3-2 yaml_2.1.18 utf8_1.1.3 XML_3.98-1.10 [9] rlang_0.2.0 pillar_1.2.1 withr_2.1.2 BiocParallel_1.12.0 [13] matrixStats_0.53.1 GenomeInfoDbData_1.0.0 plyr_1.8.4 zlibbioc_1.24.0 [17] Biostrings_2.46.0 munsell_0.4.3 gtable_0.2.0 memoise_1.1.0 [21] Biobase_2.38.0 KernSmooth_2.23-15 readr_1.1.1 scales_0.5.0 [25] BSgenome_1.46.0 plotrix_3.7 DelayedArray_0.4.1 XVector_0.18.0 [29] Rsamtools_1.30.0 impute_1.52.0 hms_0.4.2 digest_0.6.15 [33] cli_1.0.0 tools_3.4.4 bitops_1.0-6 magrittr_1.5 [37] lazyeval_0.2.1 RCurl_1.95-4.10 tibble_1.4.2 crayon_1.3.4 [41] pkgconfig_2.0.1 Matrix_1.2-12 gridBase_0.4-7 assertthat_0.2.0 [45] rstudioapi_0.7 R6_2.2.2 GenomicAlignments_1.14.1 compiler_3.4.4
Please let me know if you need more info.
Best,
Carl Baribault
