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Top Forums Shell Programming and Scripting Randomly selecting sequences and generating specific output files Post 302786141 by Scrutinizer on Wednesday 27th of March 2013 02:22:17 AM
Old 03-27-2013
Here is a start in awk you could try. The first file is read twice solely to determine the number of records..

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 infile1 infile2

You could embed it in a shell loop that increases the iter variable ( -v iter="$loopvar" )


--

Quote:
Originally Posted by Don Cragun
In you output samples, the lines in each set of output files are all in the order in which they appeared in the input files. Is that a requirement for your output, or is it just a coincidence in the random numbers used for your example?

With truly random numbers, the output could contain more than one copy of some output lines. Is it a requirement that the output lines be unique?
Isn't that a matter of sampling with/without replacement?

Last edited by Scrutinizer; 03-28-2013 at 11:13 AM.. Reason: Added parentheses to rand and stand, to make it work in gawk
 

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BP_MUTATE(1p)						User Contributed Perl Documentation					     BP_MUTATE(1p)

NAME
mutate.pl - randomly mutagenize a single protein or DNA sequence SYNOPSIS
./mutate.pl -p 25 -i test.fa -n 5 -f swiss -o muts.swiss #or ./mutate.pl --percent=25 --input=test.fa --number=5 -output=x.fa DESCRIPTION
Randomly mutagenize a single protein or DNA sequence one or more times. Specify percentage mutated and number of resulting mutant sequences. Print mutagenized sequences to STDOUT or write to an output file. -h|--help Help -p|--percent Percent mutagenized -n|--number Number of mutant sequences created -o|--output Output file (optional) -f|--format Output format (default: fasta) -i|--input Input file FEEDBACK
User feedback is an integral part of the evolution of this and other Bioperl scripts. Send your comments and suggestions to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Brian Osborne, bosborne at alum.mit.edu perl v5.14.2 2012-03-02 BP_MUTATE(1p)
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