Hey everyone,

I've been using biomaRt to access the sequences of genes for downstream analysis. Last night, the below snippet of code was functioning just fine, but today it's no longer working. Does anyone have any ideas as to why this change?

Thanks!

library("biomaRt")
ensembl = useMart("ensembl",dataset = "hsapiens_gene_ensembl")

biomaRt::getSequence(type = "ensembl_exon_id",id = "ENSE00001582105",seqType = "gene_exon",mart = ensembl)
    Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org

biomaRt::getSequence(type = "ensembl_gene_id",id = "ENSG00000121966",seqType = "gene_exon",mart = ensembl)
    Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org

EDIT: could be an issue with the global environment or my R session in general - restarting now and trying again

I usually get better results with useEnsembl, pointing to my local mirror:

> library(biomaRt)
> ensembl <- useEnsembl("ensembl","hsapiens_gene_ensembl", mirror = "useast")
> biomaRt::getSequence(type = "ensembl_exon_id",id = "ENSE00001582105",seqType = "gene_exon",mart = ensembl)
Cache found
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1 TTTTTTTTCTTCCCTCTAGTGGGCGGGGCAGAGGAGTTAGCCAAGATGTGACTTTGAAACCCTCAGCGTCTCAGTGCCCTTTTGTTCTAAACAAAGAATTTTGTAATTGGTTCTACCAAAGAAGGATATAATGAAGTCACTATGGGAAAAGATGGGGAGGAGAGTTGTAGGATTCTACATTAATTCTCTTGTGCCCTTAGCCCACTACTTCAGAATTTCCTGAAGAAAGCAAGCCTGAATTGGTTTTTTAAATTGCTTTAAAAATTTTTTTTAACTGGGTTAATGCTTGCTGAATTGGAAGTGAATGTCCATTCCTTTGCCTCTTTTGCAGATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCTGAGTCTTCAAGTTTTCACTCCAGCTAACACAGATGTAAAAGACTTTTTTTTATACGATAAATAACTTTTTTTTAAGTTACACATTTTTCAGATATAAAAGACTGACCAATATTGTACAGTTTTTATTGCTTGTTGGATTTTTGTCTTGTGTTTCTTTAGTTTTTGTGAAGTTTAATTGACTTATTTATATAAATTTTTTTTGTTTCATATTGATGTGTGTCTAGGCAGGACCTGTGGCCAAGTTCTTAGTTGCTGTATGTCTCGTGGTAGGACTGTAGAAAAGGGAACTGAACATTCCAGAGCGTGTAGTGAATCACGTAAAGCTAGAAATGATCCCCAGCTGTTTATGCATAGATAATCTCTCCATTCCCGTGGAACGTTTTTCCTGTTCTTAAGACGTGATTTTGCTGTAGAAGATGGCACTTATAACCAAAGCCCAAAGTGGTATAGAAATGCTGGTTTTTCAGTTTTCAGGAGTGGGTTGATTTCAGCACCTACAGTGTACAGTCTTGTATTAAGTTGTTAATAAAAGTACATGTTAAACTTA
  ensembl_exon_id
1 ENSE00001582105
>