Entering edit mode
29 days ago
Bertalan_Takacs
▴
90
Hi! I have an older version of the RefSeq database and I would like to get the taxids corresponding to each assembly. My problem is that because this is an older version, some of the assemblies (606 to be exact) are already suppressed or removed. Because finding all of the ids on NCBI manually would be very tedious, I am wondering if there is a script I can use to include those assemblies.
The script I've used to get all the current ids:
esearch -db assembly -query '"Bacteria"[Organism]'| esummary | xtract -pattern DocumentSummary -def "NA" -element AssemblyAccession,Taxid -block Stat > All-bacteria-refseq-complete-assembly-info.tsv