[BioC] GenomicFeatures makeTranscriptDbFromBiomart failure

[Tim Rayner]

Hi Marc,

Thanks very much for looking into this, and also to Michael for
providing the patch. I've upgraded my GRanges package and the code now
runs with a couple of warnings:

> txdb.Hs2 <- 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 ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Warning messages:
1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels)
else paste(labels,  :
  duplicated levels will not be allowed in factors anymore
2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels)
else paste(labels,  :
  duplicated levels will not be allowed in factors anymore
3: In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) :
  chromosome lengths and circularity flags are not available for this
TranscriptDb object

So I think the problem is basically fixed. I wonder if perhaps the
issue was caused by truncated data transfers; I observed several
similar failures earlier yesterday afternoon, but in each case the
problem seemed to occur at a different point in the process.

Thanks again,

Tim

On 8 November 2011 20:16, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 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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