Shell Programming and Scripting

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA 
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGG 
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGG 
ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATAGT

ID-003 ATGGGAGCGAAGGCGTCTGTTTTGAGGGG 
ID-004 ATTTGAGCGGGGGCGTCTGTTTTGAGGGG 
ID-005 ATGGGAGCGGGGGCGTCTGTTTTGAGGGG

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

#!/bin/ksh
# SYNOPSIS
#       rso [-l line_count] [-s sequence_count] fileA fileB
# DESCRIPTION
#       The rso utility "r"andomly "s"elects "sequence_count" (default 10)
#       sequences of "line_count" (default 3) corresponding lines from "fileA"
#       and "fileB" and "o"utputs those lines to files with names:
#               Outfile1-X and Outfile2-X
#       X is a sequence number ranging from 1 through "sequence_count".
#       Leading zeros will be added to the sequence number, if needed, to make
#       all output filenames be the same length.  Lines in Outfile1-* will be
#       from "fileA" and the corresponding lines in Outfile2-* will be the
#       corresponding lines from "fileB".
#
#       Even though the output lines selected will be randomly selected, no
#       input line will be output more than once in a given sequence.
#
#       The number of lines in "fileA" and "fileB" must be the same and the
#       number of lines in the files must be greater than or equal to
#       "line_count".

# Set defaults
ec=0    # Set error code (0 -> no error)
lc=3    # Set default line_count
sc=10   # Set default sequence_count
sn=$(basename $0)       # Save script name for diagnostics

# Process command line options
while getopts l:s: opt
do      case $opt in
        (l)     lc="$OPTARG";;
        (s)     sc="$OPTARG";;
        (?)     ec=1;;
        esac
done
shift $((OPTIND - 1))

# Verify # of operands
if [ $# -ne 2 ]
then    printf "%s: 2 operands are required; %d found\n" "$sn" $#
        ec=1
fi

# If we found errors or the awk script detects an error, print a usage message
if [ $ec -ne 0 ] || ! awk -v lc="$lc" -v sc="$sc" -v sn="$sn" '
# Verify that "line_count" and "sequence_count" are positive integer values
BEGIN { if(lc !~ /^[[:digit:]]+$/ || lc < 1) {
                printf("%s: line_count (%s) must be a positive integer\n",
                        sn, lc)
                ec = 1
                exit ec
        }
        if(sc !~ /^[[:digit:]]+$/ || sc < 1) {
                printf("%s: sequence_count (%s) must be a positive integer\n",
                        sn, sc)
                ec = 2
                exit ec
        }
}
# Save input file names for diagnostics
FNR == 1 {
        fn[++fc] = FILENAME
}
# Accumulate and count input lines from both input files
{       if(FNR == NR)   f1[++c1] = $0
        else            f2[++c2] = $0
}
END {   # If we got here due to an earlier detected error, get out now
        if(ec) exit ec
        # Verify that both files contain the same numbe of lines and that
        # line_count <= # of lines in the files
        if(c1 != c2) {
                printf("%s: lines in %s (%d) must equal lines in %s (%d).\n",
                        sn, fn[1], c1, fn[2], c2)
                exit 3
        }
        if(c1 < lc) {
                printf("%s: line_count(%d) must be <= # of lines in files(%d)\n",
                        sn, lc, c1)
                exit 4
        }
        # Produce output sequences
        for(i = 1; i <= sc; i++) {
                # Set output file names
                of1 = sprintf("Outfile1-%0*d", length(sc), i)
                of2 = sprintf("Outfile2-%0*d", length(sc), i)
                # Set random list of line_count line numbers to output for this
                # output sequence
                for(j = 1; j <= lc; j++) {
                        # Find line_count distinct line numbers
                        while((k = int(rand() * c1) + 1) in list) continue
                        list[k]
                }
                # Print corresponding pairs of lines from the input files into
                # the output files and delete the printed line number from the
                # list of selected random numbers.
                for(j in list) {
                        print f1[j] > of1
                        print f2[j] > of2
                        delete list[j]
                }
                # Close the output files created for this sequence
                close(of1)
                close(of2)
        }
}' "$1" "$2" >&2
then    printf "Usage: %s [-l line_count] [-s sequence_count] fileA fileB\n" \
                "$sn" >&2
        exit 1
fi

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: