Shell Programming and Scripting

Hey,
I have a problem about how to get one section of a file?
I'm new to shell, but by reading some tutorial, I think I can use awk to do this.

my input file:

Code:

>ref|ZP_04937576.1|
ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGAD
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE
>ref|NP_253535.1|
ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGAD
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE
>ref|YP_002442811.1|
ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGAD
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE
>pdb|2VQD|A
ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGA
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE

-----------------
say I have the name "NP_253535.1", how do I return the whole thing?
note each section are begin with symbol ">"

expected output:
--------

Code:

>ref|NP_253535.1|
ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGAD
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE

Thanks a lot!!

Moderator's Comments:

code tags, please!

Code:

awk -vRS=">" '/NP_253535\.1/' file

I think sed is a more regular and friendly tool that is usually faster and easy to use. Awk has more strength in delimited many-field records. I am ot much of an awk user, and I don't think either is great about multi-line blocks, but sed is pretty good, as you can pile up lines in the buffer.

Code:

sed '
  :loop
  /^>ref|'$input'| *$/!d
  :loop2
  $b
  N
  P
  s/.*\n//
  /^>...|.*| *$/b loop
  b loop2
 ' $in_file

Narrative: sed opens $in_file and examines every line. You can see the simple commands in sed allow easy reuse. I call this sort of sed a looper script. Some sed scripts just work on one line, so I call them filter-transform scripts. If you need both at once, you can pipe one sed to the next. Sed is fast and has no size limits.

I see an awk guy bartus11 has given us a one line awk script. I could one line, I guess, but I like to make it easy to read and maintain. The '.' in your $input is the sed metachar for any char, but that does not seem a very big weakness. I used more definition on the header line, so you can have <>| in the text without side effects. Is every '^>[^|]\{3\}|[^\]\{1,99\}| *$' line a header? I may have used too much definition, with /^>ref| so I will revise -- poof! Always >...|?

I like that one.
A slight variation on a theme:

Code:

nawk -v str='NP_253535.1' '$0~str{print RS $0}' RS='>' myFile

Can RS= take a regex?

My testing machine's GNU AWK can take some kind of regex in the form of character set "[]" , for example:

Code:

[bart@linux ~]$ awk -vRS="[>|]" 'NR==2' a
ref
[bart@linux ~]$ awk -vRS="[>|]" 'NR==3' a
ZP_04937576.1
[bart@linux ~]$ awk -vRS="[>|]" 'NR==4' a

ECRINAEDPKTFMPSPGKVKHFHAPGGNGVRVDSHLYSGYSVPPNYDSLVGKVITYGAD
DEALARMRNALDELIVDGIKTNTELHKDLVRDAAFCKGGVNIHYLE

After testing some more, I think any regex can go there

Great, you an make the RS proof against a > in the text somewhere! Does it take *, too? Do you lose the RS if you expand it?