BiomaRt error: Error in martCheck

Question

I am experiencing an error while using getSequence() in biomaRt.

The code is given below:

library("biomaRt")
ensemblp <- useMart(biomart="plants_mart",host="plants.ensembl.org")
osj = useDataset("osativa_eg_gene", mart = ensemblp)
genes <- read.csv("osj.csv")
osj_id <- genes$ensembl_transcript_id

os_genes <- getSequence(id = osj_id, type = "ensembl_transcript_id", seqType = "peptide", mart = ensemblp)

The error message I am getting is :

Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) :   
This function only works when used with the ensembl BioMart.This
function only works when used with the ENSEMBL_MART_ENSEMBL BioMart.

Did I make any mistake in code? Please help me fix the error. I tried asking this in Bioconductor support, but no one responded yet.

Answer 1

getSequence has only been enabled for the main Ensembl (vertebrates) biomaRt. This is all at the Bioconductor end. You'll need to use a getBM instead, for example:

os_genes <- getBM(attributes =c("ensembl_transcript_id", "peptide"), filters = "ensembl_transcript_id", values = osj_id, mart = osj)

Answer 2

Biomart seems to be down most of the time so i think you can parse the ensemble ID and names from the annotation file which i did as i was having similar problem .

You can use this to make a file with ensemble ID and gene names for you use

awk '{                                
    for (i = 1; i <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt