Question: rtracklayer export: enable trackline for GRanges and RleLists, etc?
0
gravatar for Janet Young
5.5 years ago by
Janet Young730
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young730 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
• 1.2k views
ADD COMMENTlink modified 5.5 years ago by Michael Lawrence11k • written 5.5 years ago by Janet Young730
Answer: rtracklayer export: enable trackline for GRanges and RleLists, etc?
0
gravatar for Michael Lawrence
5.5 years ago by
United States
Michael Lawrence11k wrote:
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.5 years ago by Michael Lawrence11k
nice! Thanks very much for the quick response, Michael Janet On Apr 2, 2014, at 1:25 PM, Michael Lawrence wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 5.5 years ago by Janet Young730
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 202 users visited in the last hour