#!/bin/bash
echo 1. Extract DNA fastq
awk 'NR%4==2' $1 > d.90.a
awk 'NR%4==0' $1 > d.90.q
cat d.90.q | grep -n [\"\'\^\$\#\@\!\%\&\*\(\)\+\] > d.90.v
awk 'NR%2==0' $1 > d.90.p
cat d.90.q | grep  -nv [\"\'\^\$\#\@\!\%\&\*\(\)\+\] > d.90.n
cat d.90.n | cut -d':' -f1 > d.90.m
cat d.90.v | cut -d':' -f1 > d.90.w
awk 'FNR == NR { h[$1]; next } !(FNR in h)' d.90.w d.90.a > d.b.$1
echo 2. Reverse sequence every other line 
#awk '{print>"line-"NR%$1}' d.b.$1 > d.c.$1
#echo %2, even or odd etc, input file, output file
#awk 'NR%$1==2' d.b.$1 > d.c.$1
awk '
function reverse(s,    r) {
  for (i=length(s); i>0; i--)
    r=r substr (s, i, 1);
  return r
}
{ 
  print ((NR%2) ? $0: reverse($0))
}' d.b.$1 > d.c.$1

echo Skipping ... 3. Limit line chars to 254
# This segment takes forever to process...looking for help
#cat d.c.$1 | egrep -o '(.){1,254}' > d.$1
mv d.c.$1 dna.$1
#echo 4. Twomers to HexDec to Dec
#cat d.c.$1 | hexdump| cut -c9- | awk -Wposix '{printf("%d\n","0x" $1)}' | sed 's/0//' | sed '/^$/d' > $1.dec.dat
echo Skip Cleaning up the mess!
rm d.*