Shell Programming and Scripting

Col1 Col2 Col3 Col4 Col5 Col6
A  1  A  -9  0  -9
B  2   T  -9  -9  -9
C  3   D  -9  1   -9
D  4   R  -9  2   -9

A   1   A  0 
B   2    T  -9
C   3    D  1
D   4    R   2

awk '{$4=$5}NF=4' infile

cut -d" " -f 4,6 --complement infile >outfile

mv outfile file

#!/bin/bash
infile="$1"
DELIM=$'\t'                         ### this is a tab, but it could be also a space: check your input file,
                                    ### and set it accordingly. It must be one single char only, though.

COLS=$(head -n1 "$infile" | wc -w)  ### How many columns are there in your file?
declare -a DISCARD
for ((n=1;n<=$COLS;n++)); do
 if [[ "$(cut -d "$DELIM" -f $n "$infile" | uniq)" = "-9" ]]; then
  DISCARD+=( $n )
 fi
done
cut -d "$DELIM" -f $(IFS="," echo "${DISCARD[*]}") --complement "$infile"
exit 0

awk '
  NR==FNR{
    if(NR>1){
      for(i=1;i<=NF;i++) if($i==-9) A[i]++
      m++
    }
    next
  }
  {
    for(i=1;i<=NF;i++) if(A[i]==m) $i=x
    $0=$0
    $1=$1
  }
  1
' file file