[BioC] GenomicFeatures makeTranscriptDbFromBiomart failure

[Tim Rayner]

Hi,

I'm trying to make a TranscriptDb from the Ensembl human Biomart, but
I've run into a problem. As shown below, the equivalent operation for
the mouse Biomart works fine:

> # Mouse TranscriptDb created without a hitch:
> txdb.Mm <- makeTranscriptDbFromBiomart(biomart='ensembl', dataset='mmusculus_gene_ensembl')
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK

> # Here's the problem:
> txdb.Hs <- makeTranscriptDbFromBiomart(biomart='ensembl', dataset='hsapiens_gene_ensembl')
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... Error in
scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 800380 did not have 11 elements

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicFeatures_1.6.1 AnnotationDbi_1.16.0  Biobase_2.14.0
[4] GenomicRanges_1.6.1   IRanges_1.12.1

loaded via a namespace (and not attached):
 [1] BSgenome_1.22.0    Biostrings_2.22.0  DBI_0.2-5          RCurl_1.6-10
 [5] RSQLite_0.10.0     XML_3.4-3          biomaRt_2.10.0     rtracklayer_1.14.1
 [9] tools_2.14.0       zlibbioc_1.0.0

I don't know if this is an issue with the Biomart instance or the
GenomicFeatures package. I was wondering if anyone had any suggestions
as to how I might work around this?

On a related note, would it be possible to add the ability to point
makeTranscriptDbFromBiomart() at alternate Biomart hosts (as one
would, for example, by calling
biomaRt::useMart(host='www.ensembl.org', ...))? It would probably be
good to be able to pass through the 'archive' argument to useMart as
well.

Many thanks,

Tim Rayner

-- 
Bioinformatician
Smith Lab, CIMR
University of Cambridge