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Full Discussion: Help in awk/bash
Top Forums Shell Programming and Scripting Help in awk/bash Post 302750121 by Don Cragun on Monday 31st of December 2012 02:15:22 AM
Old 12-31-2012
Quote:
Originally Posted by bioinfo
Hi,
Thanks a lot , I have done it. Smilie
I have got the following output for all files (just showing for one file and naming it as o.txt) :
100.000 0.51332 0.0000001923 -191.04738 a.txt
2000.000 0.49573 0.0000015512 -191.40071 a.txt
1000.000 0.51047 0.0000028339 -190.92254 a.txt

Further, I need your help. I have 10 more files, all of same format (11.txt) as follows, showing 2 repeats from this file:
ATOM 1 N SER A 1 35.092 83.194 140.076 1.00 0.00 N
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C
ATOM 3 C SER A 1 36.530 84.485 138.538 1.00 0.00 C
TER
ENDMDL
ATOM 1 N SER A 1 35.683 81.326 139.778 1.00 0.00 N
ATOM 2 CA SER A 1 35.422 82.736 139.929 1.00 0.00 C
ATOM 3 C SER A 1 36.497 83.588 139.247 1.00 0.00 C
TER
ENDMDL

ENDMDL is coming around 10000 times in each file. If I give input of 100 at $1 from o.txt, then it should output the first repeat from 11. txt ending with ENDMDL.
ATOM 1 N SER A 1 35.092 83.194 140.076 1.00 0.00 N
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C
ATOM 3 C SER A 1 36.530 84.485 138.538 1.00 0.00 C
TER
ENDMDL

So, corresponding to first column of o.txt, I want to retreive the repeat at the number $1/100 from 11.txt i.e. if $1=2000, then I want to retreive the pattern where ENDMDL is at 20 place.


Please guide me.

Thanks again

---------- Post updated at 10:40 PM ---------- Previous update was at 09:52 PM ----------

Please guide me. Its urgent. Smilie

Thanks
First, let me be very clear: I am a volunteer in this forum. Nothing that you ask me to do is urgent. If you need me to consider stuff that you'd like me to do for you urgent, you need to put me on your payroll!

I'm not sure I understand what you want. Am I correct in making the following assumptions:
  1. The input for this assignment is a file named o.txt.
  2. The first field of each line in o.txt is of the form x00.000 with 1 <= x <= 10000.
  3. For each line read from o.txt, the xth entry from file 11.txt is to be written to standard output where each entry in 11.txt is terminated by a line containing only ENDMDL.
  4. In addition to 11.txt, there are 9 more files like it in the same format as 11.txt that are to be ignored.
  5. You have already verified that the value in the first field of o.txt will correspond to an existing entry in 11.txt (i.e., I don't need to worry about negative values in the 1st field of o.txt, values in that field that don't end with "00.000", nor values before the "00.000" that identify a number greater than the number of times "ENDMDL" appears in 11.txt).
Are these assumptions correct?

If the above assumptions are all correct, the following script should do what you want:
Code:
#!/bin/ksh
awk 'BEGIN {rc = 1}
FNR == NR {r[rc] = r[rc] $0 "\n"
        if($0 == "ENDMDL") rc++
        next}
{       printf("%s", r[$1])}' 11.txt FS='00[.]000' o.txt

As always, if you're using a Solaris system, use /usr/xpg4/bin/awk or nawk instead of awk.

On some awk implementations, setting the array r could be simplified by setting RS to "ENDMDL" before processing 11.txt, but the standards only define the behavior when RS is set to a single character or to the empty string. The awk on OS X (which I use for testing when I'm working on solutions for issues raised in this forum) is one of the implementations that only uses the first character of RS values as the record separator.
Last edited by Don Cragun; 12-31-2012 at 05:09 AM.. Reason: Add possible solution.
This User Gave Thanks to Don Cragun For This Post:
bioinfo
 

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