Re: [0.5 OT] How to grab some entry by command line

[lina <lina.lastname@gmail.com>]

I have been following this thread, thanks all.

The uzbl one is great.

About which solutions I have found, well, the NCBI they provide some clients, there is one package, namely, ncbi-blast in debian.

I tried, but still have not figured out the right way of using it in the last two days.

On Fri, Jun 13, 2014 at 10:42 PM, <davidson@ling.ohio-state.edu> wrote:

On Thu, 12 Jun 2014, davidson@ling.ohio-state.edu wrote:

On Thu, 12 Jun 2014, lina wrote:

Hi,

I wish to grab part of the CDS entry from

http://www.ncbi.nlm.nih.gov/nuccore/KF699528.2

namely,

"MLDHSSVNSTIAPGNLLNLPVWCYLLETEEGPILVDTGMPESAV
                    NNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAF
                    TNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQ
                    SLFIETEQSGSILLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVAKEKPIIF
                    FGHDIEQEKGCKVFPEYIPRAE"

[snip]

so it is going to be nice to know how to get these html plain file which
contains these sequence,

can anyone points out something to let me go further,

using uzbl browser, along with either of the scripts on this page...

     http://www.uzbl.org/wiki/dump

...i think this can be done.  (you can have your choice of html or
plain text.)

PS: btw, uzbl has a relatively steep learning curve.

if you are in a hurry, here is a cludge that should do what you want:

jarjar@hell:~$ nuccore_fname=KF699528.2
jarjar@hell:~$ uzbl http://www.ncbi.nlm.nih.gov/nuccore/${nuccore_fname} 2>${nuccore_fname}_uzbl_squawks &
[1] 2768
jarjar@hell:~$ uzbl_pid=$!
jarjar@hell:~$ echo 'js document.documentElement.outerHTML' | socat - unix-connect:/tmp/uzbl_socket_${uzbl_pid} > ${nuccore_fname}_done.html
jarjar@hell:~$ grep -A 4 '/translation=' ${nuccore_fname}_done.html
                     /translation="MLDHSSVNSTIAPGNLLNLPVWCYLLETEEGPILVDTGMPESAV
                     NNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHFDHAGGNGAF
                     TNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQ
                     SLFIETEQSGSILLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVAKEKPIIF
                     FGHDIEQEKGCKVFPEYIPRAE"


if uzbl's complaints about the webpage don't interest you, replace
2>${nuccore_fname}_uzbl_squawks with 2>/dev/null.

anyways, would be interesting to hear what solutions you find.

-wes


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