'ORIGIN' flag missing in GenBank files

Question

[Sej Modha]

Dear All,

I noticed that a lot of GenBank files(e.g. bacterial genomes, human genome - NC_000007.14, NC_000002.12) do not contain 'ORIGIN' flag that holds the sequence on NCBI webpage as well as eutils version of the record in GenBank format.

Just wondering if something has changed or NCBI has decided to remove sequences from GenBank files?

Answer 1

[Joseph Hughes]

How about trying something like this:

esearch -db assembly -query "Homo sapiens[ORGN] AND latest[SB]" | efetch -format docsum | xtract -pattern DocumentSummary -element AssemblyAccession SpeciesTaxid SpeciesName FtpPath_RefSeq | sed 's/,.*//' | sort -k 3,3 | tee downloaded_genomes.tsv | cut -f 4 | sed -e 's/$/\/*genomic.gbff.gz/' | wget -i /dev/stdin

It is pretty ugly and I know it used to be so easy.