refseq select id from ENSEMBL id

ropensci / rentrez

talk with NCBI entrez using R

https://docs.ropensci.org/rentrez

Other

194 stars 38 forks source link

refseq select id from ENSEMBL id #147

Closed cb4github closed 4 years ago

cb4github commented 4 years ago

Dear rentrez,

The following command sequence was provided in order to convert the included ENSEMBL id to the corresponding RefSeq Select it using the Entrez Direct client. I'd like to know if it can be implemented exclusively via rentrez.

esearch -db gene -query 'ENSG00000116260' | elink -target nuccore -name gene_nuccore_refseqrna | efilter -query 'refseq_select[filter]' | efetch -format acc

Please advise, thanks.

dwinter commented 4 years ago

Sorry for taking so long to respone to this. For the record, something like this would be possible:

gene_search <- entrez_search(db = "gene", term="ENSG00000116260")
links <- entrez_link(dbfrom="gene", db = "nuccore", id = gene_search$ids)

acc_raw <- entrez_fetch(db = "nuccore", id=links$links$gene_nuccore_refseqrna, rettype="acc"), 
cat(acc_raw,"\n")

NM_001004128.3
NM_002826.5

I'm not sure how you'd get down the ref-seq select subset, though