[Bioc-devel] AnnotationHubData Error: Access denied: 530

Hi Johannes,

We are already planning to upgrade those objects to have that
information when they are downloaded...  Sonali is actually working on
that right now.  She will probably have updated that information by the
end of the week or so.  It's a lot of files to update, but this is
already in progress.

So if you are willing to wait a few days you can probably save yourself
some headaches...


   Marc




On 04/11/2015 12:13 PM, Rainer Johannes wrote:

Hi Marc,

you're right. I'll start with option 1. For that it would however be
really nice to have the seqinfo available in the GRanges as mentioned
in my previous mail. In the meantime I'll try to fetch the chrom
lengths myself but would be nice to have all that ready in the GRanges
at some point.

cheers, jo

On 11 Apr 2015, at 00:54, Marc Carlson <mcarlson at fredhutch.org
<mailto:mcarlson at fredhutch.org>> wrote:

On 04/10/2015 12:18 PM, Rainer Johannes wrote:

dear Sonali, Herve,

On 10 Apr 2015, at 19:59, Herv? Pag?s <hpages at fredhutch.org
<mailto: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?

Hi Johannes,

So you have several options actually.  We sometimes store the files in
S3 and then send them down/cache them as requested and other times the
hub can just point to an existing ftp site (and files get
transformed/cached on the fly when users ask for them).  So you have
three choices here:

1) You could just write a function that takes in one of the processed
GRanges objects and transforms it into an EnsDb object. This should be
straightforward and is probably your easiest option since you won't have
to write a recipe OR have any code included into the AnnotationHub.  You
can basically just take advantage of the fact that these data are
already there in the hub waiting to be used.
2) You could write R code that transforms a GTF file into a sqlite file
and ALSO a recipe to call that (and create metadata) for all the GTF
files.  This will be more work than #1 since you will have to write both
a recipe and port any code that you have for generating the DB files.
But when you are done you would be able to have your resources come
right out of the AnnotationHub.
3) You could write R code to process a GRanges object into an EnsDb
object and then also write a recipe so that your data resources can be
served up directly from the AnnotationHub, but still take advantage of
what is already there (GRanges).  No new data would need to be added to
the hub since new metadata records could allow users to transform the
data into EnsDb objects on the fly.  This is an elegant solution, but it
will still take more effort than option #1.

If I were you, I would start with option #1.  That way if (after I got
that working) I still wanted things to be more elegant, then I could
then add a recipe (thus evolving the strategy into option #3...


  Marc

@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

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