[BioC] GenomicFeatures makeTranscriptDbFromBiomart failure

[Marc Carlson]

Hi Tim,

There was a small bug last week for this method caused by a decision at 
ensembl to start supporting psuedoautosomal regions, but it was fixed 
last week and should be fixed with the version of GenomicFeatures 
reported here.  I just ran your code locally 4 minutes ago and it still 
works here.  The only difference I can see is that my GRanges package is 
one version higher than yours (GenomicRanges_1.6.2).  Please update that 
package and then run it again and see if you have better luck with ensembl.

The patch that Michael mentioned actually arrived at the exact moment 
that I was testing the bug fix above which means that it has a some 
conflicts I will have to resolve, but it should be added to devel very soon.


   Marc



On 11/08/2011 03:55 AM, Michael Lawrence wrote:
> On Tue, Nov 8, 2011 at 3:19 AM, Tim Rayner<tfrayner at gmail.com>  wrote:
>
>> 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', ...))?
>
> We've submitted a patch that does just this, as well as supporting an
> attribute prefix string for selecting alternative gene models.
>
>
>> 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
>>
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