Hello BioC list. I've encountered a small problem when trying to download some tracks from UCSC with rtracklayer. Specifically, I'm trying to get the "mrna" table. The example below works great for the "refGene" table, but gives an error for the "mrna" table. Any suggestions? Thanks, Mark > library(rtracklayer) Loading required package: RCurl Loading required package: bitops > session <- browserSession("UCSC") > genome(session) <- "hg18" > options(stringsAsFactors=FALSE) > q1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, 198064461, "chr3")) > tab1 <- getTable(q1) > head(tab1[,1:5]) bin name chrom strand txStart 1 2094 NM_198565 chr3 + 197851052 2 261 NM_032898 chr3 - 197917544 3 2095 NM_017861 chr3 + 197923642 4 2095 NM_002577 chr3 + 197951124 > q2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461, "chr3")) > tab2 <- getTable(q2) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 2 elements > traceback() 5: 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) 4: read.table(f, sep = "\t", header = TRUE) 3: .local(object, ...) 2: getTable(q2) 1: getTable(q2) > sessionInfo() R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.4.1 Biostrings_2.12.8 BSgenome_1.12.3 IRanges_1.2.3 [5] XML_2.6-0 --------- library(rtracklayer) session <- browserSession("UCSC") genome(session) <- "hg18" options(stringsAsFactors=FALSE) qry1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, 198064461, "chr3")) tab1 <- getTable(qry1) head(tab1[,1:5]) qry2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461, "chr3")) tab2 <- getTable(qry2) traceback() sessionInfo() --------- ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852

On Thu, Oct 1, 2009 at 11:47 PM, Mark Robinson <mrobinson@wehi.edu.au>wrote: > Hello BioC list. > > I've encountered a small problem when trying to download some tracks from > UCSC with rtracklayer. Specifically, I'm trying to get the "mrna" table. > The example below works great for the "refGene" table, but gives an error > for the "mrna" table. > > Any suggestions? > > Looked into this and found that the table browser has a slightly different set of tracks from the browser itself. I added a trackNames method (version 1.5.19) on the UCSCTableQuery, so that it's possible to know which tracks are available. >From that, you'll see that 'mrna' needs to be 'all_mrna'. Michael > Thanks, > Mark > > > library(rtracklayer) > Loading required package: RCurl > Loading required package: bitops > > session <- browserSession("UCSC") > > genome(session) <- "hg18" > > options(stringsAsFactors=FALSE) > > q1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, > 198064461, "chr3")) > > tab1 <- getTable(q1) > > head(tab1[,1:5]) > bin name chrom strand txStart > 1 2094 NM_198565 chr3 + 197851052 > 2 261 NM_032898 chr3 - 197917544 > 3 2095 NM_017861 chr3 + 197923642 > 4 2095 NM_002577 chr3 + 197951124 > > q2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461, > "chr3")) > > tab2 <- getTable(q2) > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > : > line 1 did not have 2 elements > > traceback() > 5: 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) > 4: read.table(f, sep = "\t", header = TRUE) > 3: .local(object, ...) > 2: getTable(q2) > 1: getTable(q2) > > sessionInfo() > R version 2.9.1 (2009-06-26) > i386-apple-darwin8.11.1 > > locale: > en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.1 Biostrings_2.12.8 BSgenome_1.12.3 IRanges_1.2.3 > [5] XML_2.6-0 > > > > > > --------- > library(rtracklayer) > session <- browserSession("UCSC") > genome(session) <- "hg18" > options(stringsAsFactors=FALSE) > qry1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, > 198064461, "chr3")) > tab1 <- getTable(qry1) > head(tab1[,1:5]) > qry2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, 198064461, > "chr3")) > tab2 <- getTable(qry2) > traceback() > sessionInfo() > --------- > > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson@garvan.org.au > e: mrobinson@wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

On Mon, Oct 5, 2009 at 9:55 AM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Whoa. > > Do you still plan to have the default behavoir be just chromosome X? > Because that would be quite surprising to me... > > Thinking about this some more, this would be surprising to those just wanting to use rtracklayer to download tracks. It seems like this is becoming a more popular use case than controlling the browser from R. Thus, I made ucscTableQuery() only inherit the genome from the session, so that: > session <- browserSession() > q2 <- ucscTableQuery(session, "all_mrna") Get track 'all_mrna' within hg18:*:*-* That's version 1.5.21. Michael Marc > > > > Michael Lawrence wrote: > > Hi Mark, > > > > I was not planning on porting the fix to the released version, as it's > not > > that critical. A new Bioc release is coming soon anyway. > > > > As for the devel version, I'm guessing this is more to your liking: > > > > > >> session <- browserSession("UCSC") > >> q2 <- ucscTableQuery(session, "all_mrna") > >> q2 > >> > > Get track 'all_mrna' within hg18:*:*-* > > > > That is, you are probably not interested in the (default) chrX but the > > entire genome. I keep going back and forth on the logic for deriving the > > ranges. I made the change based on the reasoning that one will be working > > through a session, with one or more views, and end up at a region of > > interest. As the query is constructed from the session, the user would > > expect the default query range to be that of the session. In fact, this > is > > the behavior of the UCSC table browser. > > > > To get what you need, you'll want to specify the range when constructing > the > > query, e.g: > > > > > >> q2 <- ucscTableQuery(session, "all_mrna", GenomicRanges(genome = > "hg18")) > >> > > > > To get the entire genome's worth of data. I just tweaked the logic to > make > > this work in version 1.5.20. Btw, you don't need the genome<- call at the > > beginning, just do it at query construction time. > > > > Michael > > > > On Sun, Oct 4, 2009 at 3:41 PM, Mark Robinson <mrobinson@wehi.edu.au> > wrote: > > > > > >> Hi Michael. > >> > >> It looks like I'm still getting some unusual behaviour with 1.5.19 > (2.10) > >> ... and am unsuccessful with the mrna table on 1.4.1 (2.9). > >> > >> I'm sending the output for both versions below. It seems 1.5.19 is only > >> gathering results for a small region on chrX and 1.4.1 doesn't accept > the > >> "all_mrna" table. I'm using fairly old versions of R 2.9 and 2.10, but > I'd > >> guess that that is not the issue. > >> > >> Any suggestions? > >> > >> Thanks, > >> Mark > >> > >> > >> [1.4.1 -- 2.9] > >> --------------------------------- > >> > >>> library(rtracklayer) > >>> > >> Loading required package: RCurl > >> Loading required package: bitops > >> > >>> session <- browserSession("UCSC") > >>> genome(session) <- "hg18" > >>> q1 <- ucscTableQuery(session, "refGene") > >>> q1 > >>> > >> Get track 'refGene' within hg18:*:*-* > >> > >>> refGene <- getTable(q1) > >>> q2 <- ucscTableQuery(session, "all_mrna") > >>> > >> Error in normArgTrack(x, track) : Unknown track: all_mrna > >> > >>> sessionInfo() > >>> > >> R version 2.9.1 (2009-06-26) > >> i386-apple-darwin8.11.1 > >> > >> locale: > >> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 > >> > >> loaded via a namespace (and not attached): > >> [1] Biobase_2.4.1 Biostrings_2.12.9 BSgenome_1.12.3 IRanges_1.2.3 > >> [5] XML_2.6-0 > >> --------------------------------- > >> > >> > >> > >> [1.5.19 -- 2.10] > >> --------------------------------- > >> > >>> library(rtracklayer) > >>> > >> Loading required package: RCurl > >> Loading required package: bitops > >> > >>> session <- browserSession("UCSC") > >>> genome(session) <- "hg18" > >>> q1 <- ucscTableQuery(session, "refGene") > >>> q1 > >>> > >> Get track 'refGene' within hg18:chrX:151073054-151383976 > >> > >>> refGene <- getTable(q1) > >>> q2 <- ucscTableQuery(session, "all_mrna") > >>> q2 > >>> > >> Get track 'all_mrna' within hg18:chrX:151073054-151383976 > >> > >>> mrna <- getTable(q2) > >>> sessionInfo() > >>> > >> R version 2.10.0 Under development (unstable) (2009-05-22 r48594) > >> i386-apple-darwin8.11.1 > >> > >> locale: > >> [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] rtracklayer_1.5.19 RCurl_0.98-1 bitops_1.0-4.1 > >> > >> loaded via a namespace (and not attached): > >> [1] Biobase_2.5.8 Biostrings_2.13.48 BSgenome_1.13.16 > IRanges_1.3.87 > >> [5] XML_2.6-0 > >> --------------------------------- > >> > >> On 3-Oct-09, at 11:10 AM, Michael Lawrence wrote: > >> > >> > >> > >>> On Thu, Oct 1, 2009 at 11:47 PM, Mark Robinson <mrobinson@wehi.edu.au> > >>> wrote: > >>> Hello BioC list. > >>> > >>> I've encountered a small problem when trying to download some tracks > from > >>> UCSC with rtracklayer. Specifically, I'm trying to get the "mrna" > table. > >>> The example below works great for the "refGene" table, but gives an > error > >>> for the "mrna" table. > >>> > >>> Any suggestions? > >>> > >>> > >>> Looked into this and found that the table browser has a slightly > different > >>> set of tracks from the browser itself. I added a trackNames method > (version > >>> 1.5.19) on the UCSCTableQuery, so that it's possible to know which > tracks > >>> are available. > >>> > >>> From that, you'll see that 'mrna' needs to be 'all_mrna'. > >>> > >>> Michael > >>> > >>> Thanks, > >>> Mark > >>> > >>> > >>>> library(rtracklayer) > >>>> > >>> Loading required package: RCurl > >>> Loading required package: bitops > >>> > >>>> session <- browserSession("UCSC") > >>>> genome(session) <- "hg18" > >>>> options(stringsAsFactors=FALSE) > >>>> q1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, > >>>> > >>> 198064461, "chr3")) > >>> > >>>> tab1 <- getTable(q1) > >>>> head(tab1[,1:5]) > >>>> > >>> bin name chrom strand txStart > >>> 1 2094 NM_198565 chr3 + 197851052 > >>> 2 261 NM_032898 chr3 - 197917544 > >>> 3 2095 NM_017861 chr3 + 197923642 > >>> 4 2095 NM_002577 chr3 + 197951124 > >>> > >>>> q2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, > 198064461, > >>>> > >>> "chr3")) > >>> > >>>> tab2 <- getTable(q2) > >>>> > >>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, > na.strings, > >>> : > >>> line 1 did not have 2 elements > >>> > >>>> traceback() > >>>> > >>> 5: 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) > >>> 4: read.table(f, sep = "\t", header = TRUE) > >>> 3: .local(object, ...) > >>> 2: getTable(q2) > >>> 1: getTable(q2) > >>> > >>>> sessionInfo() > >>>> > >>> R version 2.9.1 (2009-06-26) > >>> i386-apple-darwin8.11.1 > >>> > >>> locale: > >>> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] Biobase_2.4.1 Biostrings_2.12.8 BSgenome_1.12.3 IRanges_1.2.3 > >>> [5] XML_2.6-0 > >>> > >>> > >>> > >>> > >>> > >>> --------- > >>> library(rtracklayer) > >>> session <- browserSession("UCSC") > >>> genome(session) <- "hg18" > >>> options(stringsAsFactors=FALSE) > >>> qry1 <- ucscTableQuery(session, "refGene",GenomicRanges(197848272, > >>> 198064461, "chr3")) > >>> tab1 <- getTable(qry1) > >>> head(tab1[,1:5]) > >>> qry2 <- ucscTableQuery(session, "mrna",GenomicRanges(197848272, > 198064461, > >>> "chr3")) > >>> tab2 <- getTable(qry2) > >>> traceback() > >>> sessionInfo() > >>> --------- > >>> > >>> > >>> ------------------------------ > >>> Mark Robinson, PhD (Melb) > >>> Epigenetics Laboratory, Garvan > >>> Bioinformatics Division, WEHI > >>> e: m.robinson@garvan.org.au > >>> e: mrobinson@wehi.edu.au > >>> p: +61 (0)3 9345 2628 > >>> f: +61 (0)3 9347 0852 > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >>> > >>> > >> ------------------------------ > >> Mark Robinson, PhD (Melb) > >> Epigenetics Laboratory, Garvan > >> Bioinformatics Division, WEHI > >> e: m.robinson@garvan.org.au > >> e: mrobinson@wehi.edu.au > >> p: +61 (0)3 9345 2628 > >> f: +61 (0)3 9347 0852 > >> ------------------------------ > >> > >> > >> > >> > >> > >> > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > [[alternative HTML version deleted]]