From accesion number to assemblies *.faa and *.pff

Question

[frenchmytoast112]

Hello everyone,

I am interested if there is an automated way to download all the assemblies found in the NCBI ftp server folder for a list of accession numbers.

For example, to go from this:

http://www.ncbi.nlm.nih.gov/nuccore/NC_010473

to this on the ftp server and download the file:

ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli/latest_assembly_versions/GCF_000019425.1_ASM1942v1/

in a automated way. Or if I download the file from NCBI Reference Sequence everything is the same?

Thanks a lot!

Answer 1

[5heikki]

You can e.g. grep your accessions from this file to get the base urls (column 20) and then:

for next in $(awk -F '\t' '{print $20}' grepdFile); do wget "$next"/*.faa.gz; done

[frenchmytoast112]

Does this means I have to download the whole database to my computer?

[Jenez]

5heikki says that if you have all the proper assembly accession id's (which can be retrieved through various ways), you can grep for them in that list he/she linked, upon which you have the full link to the files through the ftp.

It's just a matter of grabbing all the assembly accessions (for example, through eutils) and then loop through them all, grepping for the proper file locations, and finally downloading them.