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Awk to extract lines with a defined number of characters

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# 1  
Old 06-17-2010
Awk to extract lines with a defined number of characters
This is my problem, my file (file A) contains the following information:
Quote:
> ID 1
DFNSALKDNJRGNLANGKNGRIIGINREVN
> ID 2
KJDFKDSJGNIHG
> ID 3
BDSBGOBAOEURBOUEABG
> ID 4
DNFKSAD
> ID 5
KJDFKDSJGNIHG
> ID 6
BDSBGOBAOEURBOUEABG
Now, I would like to create a file (file B) containing only the lines with 10 or more characters but less than 20 with their corresponding ID:
Quote:
> ID 2
KJDFKDSJGNIHG
> ID 3
BDSBGOBAOEURBOUEABG
> ID 5
KJDFKDSJGNIHG
> ID 6
BDSBGOBAOEURBOUEABG
Then, I need to compare the entries and determine their frequency. Thus, I will generate a third file (C) with the following information:
Quote:
> ID 2; freq 2
KJDFKDSJGNIHG
> ID 3; freq 2
BDSBGOBAOEURBOUEABG
I think it could be done using AWK or grep.
Any help will be greatly appreciated.
# 2  
Old 06-17-2010
try:
Code:
$ cat x
> ID 1
DFNSALKDNJRGNLANGKNGRIIGINREVN
> ID 2
KJDFKDSJGNIHG
> ID 3
BDSBGOBAOEURBOUEABG
> ID 4
DNFKSAD
> ID 5
KJDFKDSJGNIHG
> ID 6
BDSBGOBAOEURBOUEABG
$ awk '/^>/ {R=$0}! />/ && length($0) >= 10 && length($0) < 20 {print R"\n"$0}' x
> ID 2
KJDFKDSJGNIHG
> ID 3
BDSBGOBAOEURBOUEABG
> ID 5
KJDFKDSJGNIHG
> ID 6
BDSBGOBAOEURBOUEABG
$

I didn't understand the file_c requirement.
# 3  
Old 06-17-2010
Try this:


Code:
awk '/\> ID/{x=$0 ; next}{if ( length >= 10 && length < 20 ){a[$0]++;b[x]=$0}}END {for (i in a) for (j in b) if(i==b[j]){print j "\t freq " a[i]"\n" i;break;}}' file
> ID 3   freq 2
BDSBGOBAOEURBOUEABG
> ID 2   freq 2
KJDFKDSJGNIHG


Guru.
This User Gave Thanks to guruprasadpr For This Post:
Xterra
# 4  
Old 06-17-2010
Anchar,

Your answer work very well! File C should compare each and every line and record the frequency.

Guru,

I am not getting the same result. This is what I am getting:

Quote:
$ awk '/\> ID/{x=$0 ; next}{if ( length >= 10 && length < 20 ){a[$0]++;b[x]=$0}}END {for (i in a) for (j in b) if(i==b[j]){print j "\t freq " a[i]"\n" i;break;}}' TestFas.txt
freq 2
BDSBGOBAOEURBOUEABG
# 5  
Old 06-17-2010
Hi
I think yours is a sun machine. Use 'nawk' in place of 'awk'. It should go fine.

Guru.
# 6  
Old 06-17-2010
nawk
Guru,

It did not work.

Quote:
$ nawk '/\> ID/{x=$0 ; next}{if ( length >= 10 && length < 20 ){a[$0]++;b[x]=$0}}END {for (i in a) for (j in b) if(i==b[j]){print j "\t freq " a[i]"\n" i;break;}}' TestFas.txt
-bash: nawk: command not found
# 7  
Old 06-17-2010
Hi
Which is your unix flavor? Try 'gawk' if Linux.

Guru.
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