getSequence => missing attributes for your exportable?

[nick-youngblut]

Works without issue for all genes that I've tried:

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getSequence(
    id = gene_id$ensembl_gene_id,
    type = "ensembl_gene_id",
    seqType = "peptide", 
    mart = ensembl
)

Does not work for any gene that I've tried:

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getSequence(
    id = gene_id$ensembl_gene_id,
    type = "ensembl_gene_id",
    seqType = "gene_exon_intron",
    mart = ensembl
)

The error:

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable? 
Traceback:

1. getSequence(id = gene_id$ensembl_gene_id, type = "ensembl_gene_id", 
 .     seqType = "gene_exon_intron", mart = ensembl)
2. .getSequenceFromId(id, type, seqType, upstream, downstream, mart, 
 .     useCache = useCache, verbose = verbose)
3. getBM(attributes = c(seqType, type), filters = filters, mart = mart, 
 .     checkFilters = FALSE, verbose = verbose, useCache = useCache)
4. .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, 
 .     quote = quote, numAttributes = length(attributes))
5. stop(postRes)

Is this a possible issue with seqType = "gene_exon_intron"? If not, it would be helpful to have a more informative error message, or at least some more docs in getSequence() on any special considerations needed for seqType = "gene_exon_intron".

sessionInfo

R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/nickyoungblut/miniforge3/envs/seurat-v5/lib/libopenblasp-r0.3.27.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.58.0  ArcRUtils_0.1.0 ggplot2_3.5.1   tidyr_1.3.1    
[5] dplyr_1.1.4    

loaded via a namespace (and not attached):
 [1] KEGGREST_1.42.0         gtable_0.3.5            Biobase_2.62.0         
 [4] vctrs_0.6.5             tools_4.3.3             bitops_1.0-7           
 [7] generics_0.1.3          curl_5.1.0              stats4_4.3.3           
[10] tibble_3.2.1            fansi_1.0.6             AnnotationDbi_1.64.1   
[13] RSQLite_2.3.4           blob_1.2.4              pkgconfig_2.0.3        
[16] dbplyr_2.5.0            S4Vectors_0.40.2        uuid_1.2-0             
[19] lifecycle_1.0.4         GenomeInfoDbData_1.2.11 compiler_4.3.3         
[22] stringr_1.5.1           Biostrings_2.70.1       progress_1.2.3         
[25] munsell_0.5.1           repr_1.1.7              GenomeInfoDb_1.38.1    
[28] htmltools_0.5.8.1       RCurl_1.98-1.14         pillar_1.9.0           
[31] crayon_1.5.2            cachem_1.1.0            tidyselect_1.2.1       
[34] digest_0.6.35           stringi_1.8.4           purrr_1.0.2            
[37] fastmap_1.2.0           grid_4.3.3              colorspace_2.1-0       
[40] cli_3.6.2               magrittr_2.0.3          base64enc_0.1-3        
[43] XML_3.99-0.16.1         utf8_1.2.4              IRdisplay_1.1          
[46] withr_3.0.0             rappdirs_0.3.3          filelock_1.0.3         
[49] prettyunits_1.2.0       scales_1.3.0            IRkernel_1.3.2         
[52] bit64_4.0.5             XVector_0.42.0          httr_1.4.7             
[55] bit_4.0.5               pbdZMQ_0.3-11           png_0.1-8              
[58] hms_1.1.3               memoise_2.0.1           evaluate_0.23          
[61] IRanges_2.36.0          BiocFileCache_2.10.1    rlang_1.1.3            
[64] glue_1.7.0              DBI_1.2.3               xml2_1.3.6             
[67] BiocGenerics_0.48.1     jsonlite_1.8.8          R6_2.5.1               
[70] zlibbioc_1.48.0 

[grimbough]

As you surmise, this seems to be an issue with requesting the gene_exon_intron attribute. The error message you see is directly from the BioMart server. If we take biomaRt out of the equation, we can see it in the browser interface or via wget:

wget -q -O - 'https://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" uniqueRows="1" count="0" datasetConfigVersion="0.6" header="1" formatter="TSV" requestid="biomaRt">
  <Dataset name="hsapiens_gene_ensembl">
    <Attribute name = "gene_exon_intron"/>
    <Attribute name = "ensembl_gene_id"/>
    <Filter name = "ensembl_gene_id" value = "ENSG00000006062" />
  </Dataset>
</Query>' 

Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable?

This seems to be an anomaly introduced in the latest Ensembl release, as the same query works fine for Ensembl 111 from January 2024.

wget -q -O - 'https://jan2024.archive.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" uniqueRows="1" count="0" datasetConfigVersion="0.6" header="1" formatter="TSV" requestid="biomaRt">
  <Dataset name="hsapiens_gene_ensembl">
    <Attribute name = "gene_exon_intron"/>
    <Attribute name = "ensembl_gene_id"/>
    <Filter name = "ensembl_gene_id" value = "ENSG00000006062" />
  </Dataset>
</Query>' | head -n 1
Unspliced (Gene)	Gene stable ID

I would suggest contacting the Ensembl helpdesk to raise this issue with them - https://www.ensembl.org/Help/Contact

[nick-youngblut]

Apparently, a classic case of the underlying API service changing, which breaks the R, Python, etc. wrappers that use the service.

Thanks for the info!

[grimbough]

Yes, exactly. I've sent a ticket to the Ensembl helpdesk. This only seems to affect this specific sequence type and only for the human genes dataset, so hopefully it's some simple oversight that can easily be fixed server side.