Hi,

I am trying to use biomaRt to query the ensembl database for all SNPs in
the 5'UTR for a list of ensembl transcripts. Here is my code:

  SNP.germline = getBM(
    attributes = c("ensembl_transcript_id", "external_id",
"chromosome_location"),
    filters = c("so_parent_name","ensembl_transcript_id"),
    values = list("5_prime_UTR_variant",utr5$transcript_id[1:10]),
    verbose = TRUE,
    mart = ens)

This worked before, but now I am getting the following error:

> Error in getBM(attributes = c("ensembl_transcript_id", "external_id",  :
>   Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: You have an error in your SQL syntax; check the manual that
> corresponds to your MySQL server version for the right syntax to use near
> 'AND
> (hsapiens_gene_ensembl__mart_transcript_variation__dm.consequence_types_2076'
> at line 1


I should add that the "ens" mart is  the basic ensembl biomart. I use the
ens biomart earlier in the code to generate a list of relevant transcripts,
which stored as utr5$transcript_id. I don't want to use the "snp" mart
because (1) it doesn't let me filter on transcript_id, only gene_id, and
(2) it's slow

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