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Extract specific content from a file

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# 1  
Old 10-07-2009
Extract specific content from a file
My input file:
Code:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG

My desired output file:
Code:
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS

I only want to extract the header of sequence_2 and its content.
Do anybody got idea how to do it?
Will awk response faster if got a long list of contents?
Thanks for all of your suggestion Smilie
Last edited by radoulov; 10-07-2009 at 07:55 AM.. Reason: Use code tags, please!
# 2  
Old 10-07-2009
Code:
sed -n -e '/>sequence_3/q' -e '/>sequence_2/,/>sequence_3/p' t1

Put your input & output in code tags for better visibility.
# 3  
Old 10-07-2009
Hi thegeek,
Thanks for your suggestion. It is worked nice.
Can you roughly explain about the reason that you write the code?!
Code:
sed -n -e '/>sequence_3/q' -e '/>sequence_2/,/>sequence_3/p' t1

For example, if I got long list of contents and I only want to extract specific contents based on the interested header, can I use the sed code that you recommend as well?

Quote:
Originally Posted by thegeek
Code:
sed -n -e '/>sequence_3/q' -e '/>sequence_2/,/>sequence_3/p' t1

Put your input & output in code tags for better visibility.
# 4  
Old 10-09-2009
The idea is very simple,

Print from sequence_2 to sequence_3, and when you find a pattern sequence_3 just exit.

So i would very well recommend, as after the sequence_3 your file is not read, sed had been quit, so it is efficient too, is it not ?!

> This terminology in sed is PATTERN addressing.
# 5  
Old 10-09-2009
Thanks a lot, thegeek.
I understand it now d Smilie
hehe...
Do you have any idea to solve this thread:
https://www.unix.com/shell-programmin...#post302360533
It seems like more difficult and complicated Smilie
Thanks a lot for your advice.
# 6  
Old 10-10-2009
Hi Radoulov

Once again I am baffled by the brevity of your code! Smilie

You Explained this one to me a few days ago in another post: -

Code:
awk '/_3$/{exit}/_2$/{f=1}f' file

I just don't get these two at all though, why do they work?

Code:
awk '/_3$/{exit}/_2$/,0' infile

Or:

Code:
awk '/_3$/{exit}/_2$/,_' infile


What is the ,0 and ,_ about?
Last edited by steadyonabix; 10-10-2009 at 03:55 AM.. Reason: code tags
# 7  
Old 10-10-2009
Quote:
Originally Posted by steadyonabix
What is the ,0 and ,_ about?
0 is NULL and _ variable is not set, is NULL.
Literal awk will print from first pattern to the end(NULL) but exit on second pattern.

That's why I like radoulov solutions, you have to ask yourself why Smilie
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