On Thu, Aug 1, 2013 at 7:39 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > and, continuing on this important new resource, shouldn't the following > work? > >> class(x) > [1] "AnnotationHub" > attr(,"package") > [1] "AnnotationHub" >> x > class: AnnotationHub > length: 7855 > filters: none > hubUrl: http://annotationhub.bioconductor.org/ah > snapshotVersion: 2.13; snapshotDate: 2013-06-26 > hubCache: /Users/stvjc/.AnnotationHub >> keys(x, keytype="Description") > > Enter a frame number, or 0 to exit > > 1: keys(x, keytype = "Description") > 2: keys(x, keytype = "Description") > 3: .local(x, keytype, ...) > 4: .keys(snapshotUrl(x), keytype) > 5: unique(.parseJSON(url)) > 6: .parseJSON(url) > 7: tryCatch({ > tmp <- tempfile() > if (getOption("AnnotationHub.debug", FAL > 8: tryCatchList(expr, classes, parentenv, handlers) > 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) > 10: value[[3]](cond) > This is fixed now. Thanks. Dan > i'd also suggest that ahinfo() return an object, not end with a message. > >> sessionInfo() > R version 3.0.1 Patched (2013-06-02 r62857) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] > en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII > > attached base packages: > [1] parallel stats graphics grDevices datasets utils tools > [8] methods base > > other attached packages: > [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 > [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 > [7] digest_0.6.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 > [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 > [7] stats4_3.0.1 XVector_0.1.0 > > > > On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen < > kasperdanielhansen at gmail.com> wrote: > >> Hijacking the thread to discuss TAB completion as well. >> >> hub = AnnotationHub() >> hub$<tab> >> # looks good, let me try goldenpath >> hub$goldenpath.<tab> >> hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] >> hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] >> hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] >> hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] >> hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] >> hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] >> hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] >> hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] >> hub$goldenpath.vicPac1.database. ... [14] >> hub$goldenpath.xenTro ... [34] >> >> This is a bit useless, since mostly I see single letters. I would suggest >> the following >> >> First, the names tend to be super long. So don't start the examples with >> the entire path, like >> hub$goldenpath.a >> but perhaps something like >> "current selection: goldenpath. >> a.. [59] >> b.. [110] >> etc, so that goldenpath is only listed once. That way, the suggestions are >> shorter and it is clearer what the choices are between (at least I think >> that is the case) >> >> Now, when I go down the list to >> hub$goldenpath.hg19.encodeDCC.wgEncode >> >> I get >> >> Possible completions are: >> hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] >> hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroadHis tone ... >> [280] >> hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] >> hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAffy Exon ... >> [107] >> hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode ... [4] >> hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] >> hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] >> hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage ... [108] >> hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] >> hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] >> >> But for example, for wgEncodeA, it turns out that there are only two real >> choices: >> hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip ... >> [52] >> hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase ... >> [124] >> >> but I can't really see this. >> >> Anyway, I know this is hard to program, but right now it is a bit hard to >> explore using the TAB completion. Perhaps this can all be fixed by having >> more suggestions (there is probably a limited to how many suggestions to >> show). In this particular case, with this many choices of resources, I >> guess I would rather have (many) more suggestions than fewer. >> >> At the end I just did >> print(names(hub)) >> and looked at that, which is probably not what we want. >> >> Best, >> Kasper >> >> >> >> On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < >> kasperdanielhansen at gmail.com> wrote: >> >> > Technically yes, since I can do >> > >> > function(path) { >> > `[[`(hub, path) >> > } >> > >> > Still, I think it does make sense to have something a bit more standard >> (I >> > find the `[[` to be a bit unusual, but that may be colored by how I >> > program). >> > >> > Retrieving multiple resources in a single call, like >> > paths = names(hub)[1:10] >> > is going to be used a lot, I predict. >> > >> > Kasper >> > >> > >> > >> > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> > >> >> Hi Kasper, >> >> >> >> I think you could just do the following: >> >> >> >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** >> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] >> >> >> >> Instead of using $ like usual: >> >> >> >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** >> >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData >> >> >> >> >> >> Does that solve your problem? >> >> >> >> >> >> Marc >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: >> >> >> >>> I was wrong about ahinfo. Is there an exposed interface to getting the >> >>> result of a path, assuming the path is a character vector. I see I can >> >>> do >> >>> AnnotationHub:::.getResource(**hub, path) >> >>> with hub an AnnotationHub and path a character vector. >> >>> >> >>> Such an interface would be extremely useful. >> >>> >> >>> >> >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < >> >>> kasperdanielhansen at gmail.com> wrote: >> >>> >> >>> About ?AnnotationHub (package version 1.1.8) >> >>>> >> >>>> All the functions whose values are described under "Value" are not >> >>>> described under "Usage". All the functions listed under "Usage" are >> not >> >>>> described under "Value". >> >>>> >> >>>> The ahinfo (which seems to be a key function for doing things >> >>>> programmatically) is not described under either "usage" or "value". >> >>>> >> >>>> The examples are great though. >> >>>> >> >>>> Best, >> >>>> Kasper >> >>>> >> >>>> [[alternative HTML version deleted]] >> >>> >> >>> ______________________________**_________________ >> >>> Bioconductor mailing list >> >>> Bioconductor at r-project.org >> >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >>> Search the archives: http://news.gmane.org/gmane.** >> >>> science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >>> >> >> >> >> ______________________________**_________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor< >> https://stat.ethz.ch/mailman/listinfo/bioconductor> >> >> Search the archives: http://news.gmane.org/gmane.** >> >> science.biology.informatics.**conductor< >> http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> >> > >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On 08/01/2013 07:39 PM, Vincent Carey wrote: > and, continuing on this important new resource, shouldn't the > following work? > > > class(x) > [1] "AnnotationHub" > attr(,"package") > [1] "AnnotationHub" > > x > class: AnnotationHub > length: 7855 > filters: none > hubUrl: http://annotationhub.bioconductor.org/ah > snapshotVersion: 2.13; snapshotDate: 2013-06-26 > hubCache: /Users/stvjc/.AnnotationHub > > keys(x, keytype="Description") > > Enter a frame number, or 0 to exit > > 1: keys(x, keytype = "Description") > 2: keys(x, keytype = "Description") > 3: .local(x, keytype, ...) > 4: .keys(snapshotUrl(x), keytype) > 5: unique(.parseJSON(url)) > 6: .parseJSON(url) > 7: tryCatch({ > tmp <- tempfile() > if (getOption("AnnotationHub.debug", FAL > 8: tryCatchList(expr, classes, parentenv, handlers) > 9: tryCatchOne(expr, names, parentenv, handlers[[1]]) > 10: value[[3]](cond) > > i'd also suggest that ahinfo() return an object, not end with a message. > Actually, I added an argument the other day to let it do that, although I don't expect most people will need the argument. So if you want the metadata as a list you can do this: library(AnnotationHub) ah = AnnotationHub() ahinfo(ah, path="goldenpath.hg19.encodeDCC.wgEncodeUwTfbs.wgEncodeUwTfbsMcf7CtcfS tdPkRep1.narrowPeak_0.0.1.RData", returnMeta=TRUE) And it returns a list object instead of just displaying a pretty message. I am currently using this to automagically add the metadata onto GRanges and GRangesList objects when you ask for them. Marc > > sessionInfo() > R version 3.0.1 Patched (2013-06-02 r62857) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] > en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII > > attached base packages: > [1] parallel stats graphics grDevices datasets utils tools > [8] methods base > > other attached packages: > [1] AnnotationHub_1.1.8 IRanges_1.19.19 BiocGenerics_0.7.3 > [4] BiocInstaller_1.11.4 weaver_1.27.0 codetools_0.2-8 > [7] digest_0.6.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.23.18 Biobase_2.21.6 DBI_0.2-7 > [4] GenomicRanges_1.13.35 rjson_0.2.12 RSQLite_0.11.4 > [7] stats4_3.0.1 XVector_0.1.0 > > > > On Thu, Aug 1, 2013 at 8:46 PM, Kasper Daniel Hansen > <kasperdanielhansen@gmail.com <mailto:kasperdanielhansen@gmail.com="">> > wrote: > > Hijacking the thread to discuss TAB completion as well. > > hub = AnnotationHub() > hub$<tab> > # looks good, let me try goldenpath > hub$goldenpath.<tab> > hub$goldenpath.a ... [59] hub$goldenpath.b ... [110] > hub$goldenpath.c ... [257] hub$goldenpath.d ... [242] > hub$goldenpath.e ... [51] hub$goldenpath.f ... [88] > hub$goldenpath.g ... [85] hub$goldenpath.h ... [5005] > hub$goldenpath.l ... [18] hub$goldenpath.m ... [250] > hub$goldenpath.nomLeu ... [23] hub$goldenpath.o ... [68] > hub$goldenpath.p ... [175] hub$goldenpath.r ... [78] > hub$goldenpath.s ... [87] hub$goldenpath.t ... [55] > hub$goldenpath.vicPac1.database. ... [14] > hub$goldenpath.xenTro ... [34] > > This is a bit useless, since mostly I see single letters. I would > suggest > the following > > First, the names tend to be super long. So don't start the > examples with > the entire path, like > hub$goldenpath.a > but perhaps something like > "current selection: goldenpath. > a.. [59] > b.. [110] > etc, so that goldenpath is only listed once. That way, the > suggestions are > shorter and it is clearer what the choices are between (at least I > think > that is the case) > > Now, when I go down the list to > hub$goldenpath.hg19.encodeDCC.wgEncode > > I get > > Possible completions are: > hub$goldenpath.hg19.encodeDCC.wgEncodeA ... [176] > hub$goldenpath.hg19.encodeDCC.wgEncodeBroadHistone.wgEncodeBroad Histone > ... > [280] > hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041] > hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeA ffyExon > ... > [107] > hub$goldenpath.hg19.encodeDCC.wgEncodeGencodeV4.wgEncodeGencode > ... [4] > hub$goldenpath.hg19.encodeDCC.wgEncodeHaib ... [736] > hub$goldenpath.hg19.encodeDCC.wgEncodeOpenChrom ... [193] > hub$goldenpath.hg19.encodeDCC.wgEncodeRikenCage.wgEncodeRikenCage > ... [108] > hub$goldenpath.hg19.encodeDCC.wgEncodeS ... [452] > hub$goldenpath.hg19.encodeDCC.wgEncodeU ... [1394] > > But for example, for wgEncodeA, it turns out that there are only > two real > choices: > hub$goldenpath.hg19.encodeDCC.wgEncodeAffyRnaChip.wgEncodeAffyRnaChip > ... > [52] > hub$goldenpath.hg19.encodeDCC.wgEncodeAwgDnaseUniform.wgEncodeAwgDnase > ... > [124] > > but I can't really see this. > > Anyway, I know this is hard to program, but right now it is a bit > hard to > explore using the TAB completion. Perhaps this can all be fixed > by having > more suggestions (there is probably a limited to how many > suggestions to > show). In this particular case, with this many choices of > resources, I > guess I would rather have (many) more suggestions than fewer. > > At the end I just did > print(names(hub)) > and looked at that, which is probably not what we want. > > Best, > Kasper > > > > On Thu, Aug 1, 2013 at 8:35 PM, Kasper Daniel Hansen < > kasperdanielhansen@gmail.com > <mailto:kasperdanielhansen@gmail.com>> wrote: > > > Technically yes, since I can do > > > > function(path) { > > `[[`(hub, path) > > } > > > > Still, I think it does make sense to have something a bit more > standard (I > > find the `[[` to be a bit unusual, but that may be colored by how I > > program). > > > > Retrieving multiple resources in a single call, like > > paths = names(hub)[1:10] > > is going to be used a lot, I predict. > > > > Kasper > > > > > > > > On Thu, Aug 1, 2013 at 8:14 PM, Marc Carlson <mcarlson@fhcrc.org> <mailto:mcarlson@fhcrc.org>> wrote: > > > >> Hi Kasper, > >> > >> I think you could just do the following: > >> > >> ah[["goldenpath.hg19.**encodeDCC.wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData"]] > >> > >> Instead of using $ like usual: > >> > >> ah$goldenpath.hg19.encodeDCC.**wgEncodeUwTfbs.** > >> wgEncodeUwTfbsMcf7CtcfStdPkRep**1.narrowPeak_0.0.1.RData > >> > >> > >> Does that solve your problem? > >> > >> > >> Marc > >> > >> > >> > >> > >> > >> > >> On 07/31/2013 06:14 PM, Kasper Daniel Hansen wrote: > >> > >>> I was wrong about ahinfo. Is there an exposed interface to > getting the > >>> result of a path, assuming the path is a character vector. I > see I can > >>> do > >>> AnnotationHub:::.getResource(**hub, path) > >>> with hub an AnnotationHub and path a character vector. > >>> > >>> Such an interface would be extremely useful. > >>> > >>> > >>> On Wed, Jul 31, 2013 at 9:02 PM, Kasper Daniel Hansen < > >>> kasperdanielhansen@gmail.com > <mailto:kasperdanielhansen@gmail.com>> wrote: > >>> > >>> About ?AnnotationHub (package version 1.1.8) > >>>> > >>>> All the functions whose values are described under "Value" > are not > >>>> described under "Usage". All the functions listed under > "Usage" are not > >>>> described under "Value". > >>>> > >>>> The ahinfo (which seems to be a key function for doing things > >>>> programmatically) is not described under either "usage" or > "value". > >>>> > >>>> The examples are great though. > >>>> > >>>> Best, > >>>> Kasper > >>>> > >>>> [[alternative HTML version deleted]] > >>> > >>> ______________________________**_________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > >>> > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >>> Search the archives: http://news.gmane.org/gmane.** > >>> > science.biology.informatics.**conductor<http: news.gmane.org="" gm="" ane.science.biology.informatics.conductor=""> > >>> > >> > >> ______________________________**_________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > >> > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: sta="" t.ethz.ch="" mailman="" listinfo="" bioconductor=""> > >> Search the archives: http://news.gmane.org/gmane.** > >> > science.biology.informatics.**conductor<http: news.gmane.org="" gm="" ane.science.biology.informatics.conductor=""> > >> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto: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]]