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Top Forums Shell Programming and Scripting Randomly selecting sequences and generating specific output files Post 302786545 by Xterra on Wednesday 27th of March 2013 05:25:41 PM
Old 03-27-2013
Scrutinizer,
I am afraid I do not understand your script. I get some error when trying to run the script.
Am I missing something?
X
Code:
awk -v s=3 -v iter=1 '
  NR==FNR { 
    next 
  }
  FNR==1 {
    if(!set) {
      srand;
      n=NR-1
      for(i=1; i<=s; i++) {
        line=0
        while(!line || line in A) line=int(rand*n)+1
        A[line]
      }
      set=1
    }
    close(f)
    f=FILENAME ".out" iter
  } 
  FNR in A {
    print > f
  }
' infile1.txt infile1.txt infile2.txt
awk: cmd. line:7: srand;
awk: cmd. line:7: ^ syntax error
awk: cmd. line:11: while(!line || line in A) line=int(rand*n)+1
awk: cmd. line:11: ^ syntax error
awk: cmd. line:11: while(!line || line in A) line=int(rand*n)+1
awk: cmd. line:11:

---------- Post updated at 05:25 PM ---------- Previous update was at 05:24 PM ----------

Hanson44,
Sheel scripting will be ok too.
Thanks!
X
 

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SPLIT(1)						      General Commands Manual							  SPLIT(1)

NAME
split - split a file into pieces SYNOPSIS
split [ option ... ] [ file ] DESCRIPTION
Split reads file (standard input by default) and writes it in pieces of 1000 lines per output file. The names of the output files are xaa, xab, and so on to xzz. The options are -n n Split into n-line pieces. -l n Synonym for -n n, a nod to Unix's syntax. -e expression File divisions occur at each line that matches a regular expression; see regexp(7). Multiple -e options may appear. If a subex- pression of expression is contained in parentheses (...), the output file name is the portion of the line which matches the subex- pression. -f stem Use stem instead of x in output file names. -s suffix Append suffix to names identified under -e. -x Exclude the matched input line from the output file. -i Ignore case in option -e; force output file names (excluding the suffix) to lower case. SOURCE
/src/cmd/split.c SEE ALSO
sed(1), awk(1), grep(1), regexp(7) SPLIT(1)
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