How to count files/folders on NCBI ftp server?
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5.7 years ago
Tao ▴ 460

Hi,

I log in NCBI ftp server by this way:

ftp ftp.ncbi.nih.gov

And then cd to ./genomes/refseq/.I want to check how many folders/genomes are in the refeq folder, what command should I use?

I used this way to do it:

ls . list # save to local file 'list', then use wc -l to count

do you have easier way?

Thanks, Tao

ftp ncbi linux shell • 3.1k views
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5.7 years ago
SES 8.5k

I would use a little script to handle this type of work. For example,

or the equivalent:

You can modify those to get what you need from the list.

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That's great! I like the python version! thanks so much!

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Glad I could help. You might want to add some debugging to the python because I don't think those commands will warn if they fail. There is a lot of test statements in the perl to be safe and the python should probably also have some tests.

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That's very good suggestion, thanks!

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5.7 years ago
Spencer D. • 0

you could probably just pipe instead of saving to a local file. i.e. ls -l | wc -l

disclosure: haven't checked it for bugs or reliability

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ftp> ls | wc -l usage: ls remote-directory local-file

pipe command doesn't work on ftp mode

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Ah yea I checked it on my local directory. Looks like the script would do the job for you anyways!

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