I have tried to alter the Ensembl.R script to use the correct "mart" by altering the the respective line to:
ensembl = useMart("metazoa_mart_7", dataset=paste(organism, "_eg_gene", sep=""))
which I gleaned from playing with useMart() and listDatasets() and the like. The script seems to connect to the right mart but chokes at the second stage with the following error:
It REALLY pissed me off when ensembl moved all the vector insects to a separate site but its pretty infuriating if they have also drifted from the standard DB schema which seems to make all tools built to access ensembl data useless on the metazoa.ensembl.org site! Can anyone help me here?
Gus
ensembl = useMart("metazoa_mart_7", dataset=paste(organism, "_eg_gene", sep=""))
which I gleaned from playing with useMart() and listDatasets() and the like. The script seems to connect to the right mart but chokes at the second stage with the following error:
Code:
augustine@jupiter 02:31:18 ~/work/data/myrna/refs/aedes_metazoaEnsmbl_r7: Rscript --vanilla --default-packages=base,methods,utils,stats,IRanges,biomaRt,Biostrings /home/augustine/src/myrna-1.0.9/reftools/Ensembl_metazoa.R --args aaegypti ftp://ftp.ensemblgenomes.org/pub/metazoa/release-7/fasta/aedes_aegypti 0 0 Ensembl.R [02h:32m:20s]: organism: aaegypti Ensembl.R [02h:32m:20s]: 1/11. Connecting to Ensembl via biomaRt Ensembl.R [02h:32m:36s]: 2/11. Getting table of exons (somewhat slow) Error in getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id", : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Execution halted
Gus
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