Question about rtracklayer GenomicRanges bed export order
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Last seen 9.6 years ago
Is there a way to specify order for the export.bed function in rtracklayer? I have searched but cannot find a way. Here is a simple example. Say you import a bed file, do some operation (like shift each region by 500 bp), then you want to export it, in the same order it was when you imported it. It seems to me that rtracklayer's export.bed is automatically ordering to the "natural order" of the genomic ranges -- I cannot find a way to disable this. Here's a reproducible example: gr = GRanges(seqnames=c("chr6", "chr4"), ranges=IRanges(c(1,50), c(70,90))) export.bed(gr, "gr_order.bed"); The exported file, gr_order.bed, will have the order inverted to put chr4 first. Even if you try to specify an order by subsetting gr, it still orders it how it wants. I feel like I'm missing something simple but for some reason can't track it down... -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] data.table_1.8.10 rtracklayer_1.18.2 GenomicRanges_1.10.7 IRanges_1.16.6 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1 parallel_2.15.1 RCurl_1.95-4.1 Rsamtools_1.10.2 stats4_2.15.1 tools_2.15.1 [9] XML_3.98-1.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
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@michael-lawrence-3846
Last seen 2.3 years ago
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Yea, unfortunately rtracklayer export is still completely based on RangedData, which forces the ordering by chromosome. Over this release cycle, I'll try to rewrite everything. Shouldn't be too bad. On Tue, Oct 22, 2013 at 6:29 AM, Nathan Sheffield [guest] < guest@bioconductor.org> wrote: > > Is there a way to specify order for the export.bed function in > rtracklayer? I have searched but cannot find a way. > > Here is a simple example. Say you import a bed file, do some operation > (like shift each region by 500 bp), then you want to export it, in the same > order it was when you imported it. > > It seems to me that rtracklayer's export.bed is automatically ordering to > the "natural order" of the genomic ranges -- I cannot find a way to disable > this. > > Here's a reproducible example: > > gr = GRanges(seqnames=c("chr6", "chr4"), ranges=IRanges(c(1,50), c(70,90))) > export.bed(gr, "gr_order.bed"); > > The exported file, gr_order.bed, will have the order inverted to put chr4 > first. Even if you try to specify an order by subsetting gr, it still > orders it how it wants. > > I feel like I'm missing something simple but for some reason can't track > it down... > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > LC_MONETARY=en_US.UTF-8 > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] data.table_1.8.10 rtracklayer_1.18.2 GenomicRanges_1.10.7 > IRanges_1.16.6 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1 parallel_2.15.1 > RCurl_1.95-4.1 Rsamtools_1.10.2 stats4_2.15.1 tools_2.15.1 > [9] XML_3.98-1.1 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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Ok, I have completed the refactoring. GRanges is now primary and there shouldn't be any reordering. Upcoming version 1.23.2. Michael On Tue, Oct 22, 2013 at 6:57 AM, Michael Lawrence <michafla@gene.com> wrote: > Yea, unfortunately rtracklayer export is still completely based on > RangedData, which forces the ordering by chromosome. Over this release > cycle, I'll try to rewrite everything. Shouldn't be too bad. > > > On Tue, Oct 22, 2013 at 6:29 AM, Nathan Sheffield [guest] < > guest@bioconductor.org> wrote: > >> >> Is there a way to specify order for the export.bed function in >> rtracklayer? I have searched but cannot find a way. >> >> Here is a simple example. Say you import a bed file, do some operation >> (like shift each region by 500 bp), then you want to export it, in the same >> order it was when you imported it. >> >> It seems to me that rtracklayer's export.bed is automatically ordering to >> the "natural order" of the genomic ranges -- I cannot find a way to disable >> this. >> >> Here's a reproducible example: >> >> gr = GRanges(seqnames=c("chr6", "chr4"), ranges=IRanges(c(1,50), >> c(70,90))) >> export.bed(gr, "gr_order.bed"); >> >> The exported file, gr_order.bed, will have the order inverted to put chr4 >> first. Even if you try to specify an order by subsetting gr, it still >> orders it how it wants. >> >> I feel like I'm missing something simple but for some reason can't track >> it down... >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 >> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C >> LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] data.table_1.8.10 rtracklayer_1.18.2 GenomicRanges_1.10.7 >> IRanges_1.16.6 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.26.3 bitops_1.0-6 BSgenome_1.26.1 >> parallel_2.15.1 RCurl_1.95-4.1 Rsamtools_1.10.2 stats4_2.15.1 >> tools_2.15.1 >> [9] XML_3.98-1.1 zlibbioc_1.4.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> > > [[alternative HTML version deleted]]
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