[Bioc-devel] AnnotationHubData Error: Access denied: 530
Hervé Pagès
hpages at fredhutch.org
Fri Apr 10 19:59:28 CEST 2015
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?
@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.
@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?
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
>> _______________________________________________
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>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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E-mail: hpages at fredhutch.org
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