Question: 'ORIGIN' flag missing in GenBank files
4
gravatar for Sej Modha
19 months ago by
Sej Modha3.9k
Glasgow, UK
Sej Modha3.9k wrote:

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?

eutils genbank ncbi • 499 views
ADD COMMENTlink modified 19 months ago by Joseph Hughes2.6k • written 19 months ago by Sej Modha3.9k
1
gravatar for Joseph Hughes
19 months ago by
Joseph Hughes2.6k
Scotland, UK
Joseph Hughes2.6k wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Joseph Hughes2.6k
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