[BioC] AnnotationHub man page improvements

Dan Tenenbaum dtenenba at fhcrc.org
Fri Aug 2 19:48:38 CEST 2013 

On Fri, Aug 2, 2013 at 10:46 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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.

I should have mentioned that the problem was fixed on the server side,
so you don't need to download the latest AnnotationHub, it should
"just work" now.

Dan



> 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.wgEncodeBroadHistone ...
>>> [280]
>>> hub$goldenpath.hg19.encodeDCC.wgEncodeC ... [1041]
>>> hub$goldenpath.hg19.encodeDCC.wgEncodeDukeAffyExon.wgEncodeDukeAffyExon ...
>>> [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]]
>>> >>>
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