Shell Programming and Scripting

>Data_1
ASWDADAQTWQQGSAAAAASDAFAFA
.
.

Data_1 2 Z
Data_1 3 T
Data_1 10 A
Data_1 11 T
.
.

>Data_1
AZTDADAQTATQGSAAAAASDAFAFA
.
.

awk -F "\t" '(FNR==1){x++} (x==1){a[$1][$2]=$3;next} (x==2){if($0~/>/){h=$0;sub(/^.*Data/,"",h);sub(/ .*/,"",h)} else{seq[h]=seq[h]$0}} END{for(i in a){s=0; for(j in a[i]){m=m substr(seq[i],s,j-1) a[i][j];s=j+1} m=m substr(seq[i],s); print ">Data"i"\n"m}}' File 2 File 1

awk '
        NR == FNR {
                A[">"$1 FS $2] = $3
                next
        }
        /^>/ {
                T = $0
                print
                next
        }
        {
                for ( i = 1; i <= length; i++ )
                {
                        if ( ( T FS i ) in A )
                                printf "%s", A[T FS i]
                        else
                                printf "%s", substr( $0, i, 1 )
                }
                printf "\n"
        }
' file2 file1

awk 'NR==FNR {a[$1,$2]=$2; b[$1,$2]=$3; c[$1]=$1; next}
/^>/ {w=$0; sub(".*> *", "", w)}
! /^>/ && c[w] {for (i in a) $(a[i])=b[i]}
1
' file2 FS= OFS= file1

awk '
  NR==FNR { 
    R[$1,$2]=$3
    next
  }
  FNR>1 {
    s=x
    for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1))
    print RS $1 FS s
  }
' file2 RS=\> FS='\n' file1