Shell Programming and Scripting

>A1
ACFGTSDCHG_GDF
DGHA
>A2
A_FGGSD_HG_GSF
DGTA
>A3
AC_GSDD_TU_GDF
DGH_
..
...

>A1
TC_A
>A2
G__A
>A3
S___

sed '/^>/{n;N;s/\n//;s/....\(.\)..\(.\)..\(.\)....../\1\2\3/;}' infile

awk 'NR>1{printf RS}; sub(/\n.*/,"\n" substr($2,5,1) substr($2,8,1) substr($2,11,1) substr($3,4,1) "\n")' RS=\> ORS= infile

awk 'NR>1{printf RS $1 $2 $3 $8 $11 $14 $22 "\n"}' FS= RS=\> ORS= infile

awk -vF=5,8,11,18 '
BEGIN{w=split(F,T,",")}
NR>1{
   print RS substr($0,1,3)
   gsub(/\n/,"",$0)
   for(i=1;i<=w;i++) printf "%s", substr($0,T[i]+2,1)
   printf "\n" }' RS=\> ORS= infile

awk -vF=5,8,11,18 '
BEGIN{w=split(F,T,",")}
NR>1{
   print RS $1
   a=length($1)
   gsub(/\n/,"",$0)
   for(i=1;i<=w;i++) printf "%s", substr($0,T[i]+a,1)
   print "" }' RS=\> infile