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, <david...@ling.ohio-state.edu> wrote: > On Thu, 12 Jun 2014, david...@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 >>> NNEGLFNGTFVEGQILPKMTEEDRIVNILK >>> RVGYEPDDLLYIISSHLHFDHAGGNGAF >>> TNTPIIVQRTEYEAALHREEYMKECILPHL >>> NYKIIEGDYEVVPGVQLLYTPGHSPGHQ >>> SLFIETEQSGSILLTIDASYTKENFEDEVP >>> FAGFDPELALSSIKRLKEVVAKEKPIIF >>> 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=' ${nuccore_fname}_done.html > /translation="MLDHSSVNSTIAPGNLLNLPVWCYLLETEE > GPILVDTGMPESAV > NNEGLFNGTFVEGQILPKMTEEDRIVNILK > RVGYEPDDLLYIISSHLHFDHAGGNGAF > TNTPIIVQRTEYEAALHREEYMKECILPHL > NYKIIEGDYEVVPGVQLLYTPGHSPGHQ > SLFIETEQSGSILLTIDASYTKENFEDEVP > FAGFDPELALSSIKRLKEVVAKEKPIIF > FGHDIEQEKGCKVFPEYIPRAE" > > > if uzbl's complaints about the webpage don't interest you, replace > 2>${nuccore_fname}_uzbl_squawks with 2>/dev/null. > > anyways, would be interesting to hear what solutions you find. > > > -wes > > > -- > To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a > subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: https://lists.debian.org/alpine.DEB.2.02.1406131037580. > 15...@brutus.ling.ohio-state.edu > >
