[Bioc-devel] AnnotationHubData Error: Access denied: 530
Arora, Sonali
sarora at fredhutch.org
Fri Apr 10 22:53:53 CEST 2015
Dear Johannes,
I am going to update the GRanges object ( from Ensembl's GTF files) with
the necessary information.
Once that's done, I'll post back here.
Thanks,
Sonali.
On 4/10/2015 12:18 PM, Rainer Johannes wrote:
> dear Sonali, Herve,
>
>> On 10 Apr 2015, at 19:59, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> Hi Johannes, Sonali,
>>
>> On 04/10/2015 09:40 AM, Arora, Sonali wrote:
>>> Hi Rainer,
>>>
>>> Just to be clear - what do you want to be available from AnnotationHub()
>>> in the end?
>>>
>>> Currently the GTF files from Ensembl are already present inside the
>>> AnnotationHub
>>>
>>> library(AnnotationHub)
>>> ah = AnnotationHub()
>>> gtf <- query(ah, "GTF")
>>> gtf <- query(gtf, "Ensembl")
>>> gtf[1]
>>> gtf[[1]] # returned to you as GenomicRanges object.
>>>
>>> - why not get the GTF files directly from AnnotationHub instead of
>>> getting them from the ftp site? Then you can make your EnsDb classes
>>> from these GRanges.
>>> It will also make your recipe faster because you will not have to
>>> download the file and parse the object.
>>
>> A GRanges object is not the same as a GTF file and I guess Johannes
>> wants access to the GTF file. Are these GTF files available on
>> AnnotationHub?
>>
>
> yes, you're right. I wanted access to the GTF file and most likely
> understood the AnnotationHub idea wrong... my idea was to build a
> recipe that takes as input the GTF file (as the
> makeEnsemblGtfToGRanges) and generates from that the EnsDb SQLite
> database file. I thought that these SQLite files would be generated on
> the fly on the user's computer, but I guess that stuff is processed
> once and stored on your servers, right?
>
>
>> @Johannes - Here is one alternative: You could take a different approach
>> and implement some equivalent of makeTxDbFromGRanges() for EnsDb
>> objects. So people could just do:
>>
>> library(ensembldb)
>> ensdb <- makeEnsDbFromGRanges(gtf[[1]])
>>
>> like they can do right now with makeTxDbFromGRanges():
>>
>> library(GenomicFeatures)
>> txdb <- makeTxDbFromGRanges(gtf[[1]])
>>
>> That way you don't need a recipe or try to add things to
>> AnnotationHub at all.
>>
>
> that's a good idea, I will implement that too. just want to make sure
> that I can get all data I'll need (also the genome build version,
> Ensembl version etc from the GRanges, most likely I have to guess that
> from the file name of the RData file).
>
>> @Sonali - These GRanges objects I get from AnnotationHub have no genome
>> information and their seqlevels are not sorted:
>>
>> > seqinfo(gtf[[1]])
>> Seqinfo object with 22 sequences from an unspecified genome; no
>> seqlengths:
>> seqnames seqlengths isCircular genome
>> X <NA> <NA> <NA>
>> 9 <NA> <NA> <NA>
>> 8 <NA> <NA> <NA>
>> 7 <NA> <NA> <NA>
>> 6 <NA> <NA> <NA>
>> ... ... ... ...
>> 12 <NA> <NA> <NA>
>> 11 <NA> <NA> <NA>
>> 10 <NA> <NA> <NA>
>> 1 <NA> <NA> <NA>
>> MT <NA> <NA> <NA>
>>
>> I know it's easy enough to sort the seqlevels with sortSeqlevels() but
>> what about having these things done by the recipe instead?
>>
>
> I also have a suggestion there: what if you used also
> the fetchChromLengthsFromEnsembl from the GenomicFeatures package? the
> GTF files are anyway from Ensembl, so getting the seqinfo from there
> would make sense... and I wouldn't have to fetch it separately to
> build the EnsDb.
>
> thanks!
> jo
>
>> Thanks,
>> H.
>>
>>
>>>
>>> Thanks,
>>> Sonali.
>>>
>>>
>>> On 4/9/2015 11:14 PM, Rainer Johannes wrote:
>>>> dear all,
>>>>
>>>> I have added a recipe to the AnnotationHubData to provide EnsDb
>>>> classes (from my ensembldb package) based on GTF files from Ensembl.
>>>> Now, after adding the recipe to the AnnotationHubData package and
>>>> installing it (following the vignettes from the AnnotationHub and
>>>> AnnotationHubData) I called
>>>>
>>>> updateResources(AnnotationHubRoot=getWd(), BiocVersion=biocVersion(),
>>>> preparerClasses="EnsemblGtfToEnsDbPreparer", insert=FALSE,
>>>> metadataOnly=TRUE)
>>>>
>>>> and got the output:
>>>>
>>>> Ailuropoda_melanoleuca.ailMel1.78.gtf.gz
>>>> Anas_platyrhynchos.BGI_duck_1.0.78.gtf.gz
>>>> Anolis_carolinensis.AnoCar2.0.78.gtf.gz
>>>> Astyanax_mexicanus.AstMex102.78.gtf.gz
>>>> Bos_taurus.UMD3.1.78.gtf.gz
>>>> Caenorhabditis_elegans.WBcel235.78.gtf.gz
>>>> Callithrix_jacchus.C_jacchus3.2.1.78.gtf.gz
>>>> Canis_familiaris.CanFam3.1.78.gtf.gz
>>>> Cavia_porcellus.cavPor3.78.gtf.gz
>>>> Chlorocebus_sabaeus.ChlSab1.1.78.gtf.gz
>>>> Choloepus_hoffmanni.choHof1.78.gtf.gz
>>>> Ciona_intestinalis.KH.78.gtf.gz
>>>> Ciona_savignyi.CSAV2.0.78.gtf.gz
>>>> Danio_rerio.Zv9.78.gtf.gz
>>>> Dasypus_novemcinctus.Dasnov3.0.78.gtf.gz
>>>> Dipodomys_ordii.dipOrd1.78.gtf.gz
>>>> Drosophila_melanogaster.BDGP5.78.gtf.gz
>>>> Error in function (type, msg, asError = TRUE) : Access denied: 530
>>>>
>>>> I guess that must be related to the Ensembl ftp? Is anybody else
>>>> experiencing this error?
>>>>
>>>> cheers, jo
>>>>
>>>>
>>>> my session info:
>>>>
>>>>> sessionInfo()
>>>> R Under development (unstable) (2015-03-04 r67940)
>>>> Platform: x86_64-apple-darwin14.3.0/x86_64 (64-bit)
>>>> Running under: OS X 10.10.3 (Yosemite)
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] parallel stats4 stats graphics grDevices utils
>>>> datasets
>>>> [8] methods base
>>>>
>>>> other attached packages:
>>>> [1] AnnotationHubData_0.0.205 futile.logger_1.4
>>>> [3] AnnotationHub_1.99.81 GenomicRanges_1.19.52
>>>> [5] GenomeInfoDb_1.3.16 IRanges_2.1.43
>>>> [7] S4Vectors_0.5.22 BiocGenerics_0.13.11
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] Rcpp_0.11.5 BiocInstaller_1.17.7
>>>> [3] XVector_0.7.4 futile.options_1.0.0
>>>> [5] GenomicFeatures_1.19.37 bitops_1.0-6
>>>> [7] tools_3.2.0 zlibbioc_1.13.3
>>>> [9] biomaRt_2.23.5 digest_0.6.8
>>>> [11] BSgenome_1.35.20 jsonlite_0.9.15
>>>> [13] RSQLite_1.0.0 shiny_0.11.1
>>>> [15] DBI_0.3.1 rtracklayer_1.27.11
>>>> [17] httr_0.6.1 stringr_0.6.2
>>>> [19] Biostrings_2.35.12 Biobase_2.27.3
>>>> [21] R6_2.0.1 AnnotationDbi_1.29.21
>>>> [23] XML_3.98-1.1 BiocParallel_1.1.24
>>>> [25] RJSONIO_1.3-0 ensembldb_0.99.15
>>>> [27] lambda.r_1.1.7 Rsamtools_1.19.50
>>>> [29] htmltools_0.2.6 GenomicAlignments_1.3.34
>>>> [31] AnnotationForge_1.9.7 mime_0.3
>>>> [33] interactiveDisplayBase_1.5.6 xtable_1.7-4
>>>> [35] httpuv_1.3.2 RCurl_1.95-4.5
>>>> [37] VariantAnnotation_1.13.47
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail:hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
>>
>> _______________________________________________
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>
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