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Old 07-26-2014, 09:42 AM   #1
Zapages
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Location: NJ

Join Date: Oct 2012
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Default batch download from NCBI FTP

Hi guys,

I know in linux we can do a batch download for certain files with same extension such by doing something like this

wget genomic.fna.gz ie. ftp://ftp.ncbi.nlm.nih.gov/refseq/release//bacteria/

But how would I do this in OSX with curl command.

I have tried curl -0 ftp://ftp.ncbi.nlm.nih.gov/refseq/re...genomic.fna.gz

as an example and I get 550 error as if I was getting file not found error or no permission.

But if I try curl genomic.fna.gz -0 ftp://ftp.ncbi.nlm.nih.gov/refseq/re...teria/bacteria.[??].genomic.fna.gz

I get empty files as I don't know the command to place in between in the ?? to allow it work properly to download all the of the fasta files for bacteria reference set.

Also it changes to bacteria.1.1 bacteria.2.1 bacteria.2..2 bacteria.3.1


Thank you in advance.

-Zapages
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Old 07-26-2014, 10:22 AM   #2
GenoMax
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Try this. Adjust X for the number of files you want to get. It appears there are 152 right now at the FTP link.

Code:
$ curl "ftp://ftp.ncbi.nlm.nih.gov/refseq/release//bacteria/bacteria.[1-X].1.genomic.fna.gz" -o "bacteria.#1.1.genomic.fna.gz"
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