Checked in for rtracklayer 1.23.21. Grab from svn if you need it right away.

Michael


On Wed, Apr 2, 2014 at 11:40 AM, Janet Young <jayoung@fhcrc.org> wrote:

> Hi there,
>
> I'd love to put in a request, if I can?   Using the devel version of
> tracklayer, I'd like to be able to include a trackline when I export
> GRanges, and RleLists, etc.  It looks like that's not implemented right
> now?  I know there's a manual way to do this (write a trackline to its own
> file, then append the export to that file), but it'd be really nice to have
> that functionality in the export function at some point in the future.
>
> I've included some code below to show you what I mean.
>
> thanks very much,
>
> Janet
>
> ------------
>
> library(rtracklayer)
>
> ### demo test item from ?export
> test_path <- system.file("tests", package = "rtracklayer")
> test_bed <- file.path(test_path, "test.bed")
> test <- import(test_bed, asRangedData = FALSE)
> test
>
> ## demo export from ?export: I do get a trackline in this file
> test_bed_out <- file.path(tempdir(), "test.bed")
> export(test, test_bed_out)
>
> ## for GRanges objects there's no trackline exported by default (that's
> OK):
> gr <- as(test,"GRanges")
> export(gr, test_bed_out)
>
> ### but it'd be really nice to be able to request a trackline specifically
> - it doesn't seem to be implemented right now:
> myTrackLine <- new("TrackLine", name="gr", color=col2rgb("red")[,1])
> export(gr, test_bed_out, trackLine=myTrackLine)
> # Error in .local(object, con, format, ...) :
> #   unused argument (trackLine = <S4 object of class "TrackLine">)
>
> ## same thing for SimpleRleList
> export(coverage(gr), con=test_bed_out, format="bedGraph",
> trackLine=myTrackLine)
> #Error in .local(object, con, format, ...) :
> #  unused argument (trackLine = <S4 object of class "TrackLine">)
>
> ### my own examples include bed files for GRanges objects, and bedGraph
> files for SimpleRleList, but I can imagine other examples too. Would it be
> hard to implement trackLine option for any output format where tracklines
> are acceptable?
>
> sessionInfo()
>
> R Under development (unstable) (2013-11-06 r64163)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] rtracklayer_1.23.20   GenomicRanges_1.15.42 GenomeInfoDb_0.99.26
> [4] IRanges_1.21.39       BiocGenerics_0.9.3
>
> loaded via a namespace (and not attached):
>  [1] BatchJobs_1.2             BBmisc_1.5
>  [3] BiocParallel_0.5.18       Biostrings_2.31.20
>  [5] bitops_1.0-6              brew_1.0-6
>  [7] BSgenome_1.31.12          codetools_0.2-8
>  [9] DBI_0.2-7                 digest_0.6.4
> [11] fail_1.2                  foreach_1.4.1
> [13] GenomicAlignments_0.99.36 iterators_1.0.6
> [15] plyr_1.8.1                Rcpp_0.11.1
> [17] RCurl_1.95-4.1            Rsamtools_1.15.38
> [19] RSQLite_0.11.4            sendmailR_1.1-2
> [21] stats4_3.1.0              stringr_0.6.2
> [23] tools_3.1.0               XML_3.98-1.1
> [25] XVector_0.3.7             zlibbioc_1.9.0
>
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