Shell Programming and Scripting

>tempZ_1
SAFSDAFDSG
GGERRTTZZZ
ZASRARARET
WETPOASDAZ
ZZZASASFAS

>temp_9
ASAEGPIOEO
EIOPIZZZAS
FDFGZZZARA
ESEAZZZAAS
.
.

>tempZ_1
SAFSDAFDSG
GGERRTTASR
ARARETWETP
OASDAASASF
AS

>temp_9
ASAEGPIOEO
EIOPIASFDF
GARAESEAAA
S
.
.

sed 's///g' input_file
>tempZ_1
SAFSDAFDSG
GGERRTT
 ASRARARET
WETPOASDA
   ASASFAS

>temp_9
ASAEGPIOEO
EIOPI   AS
FDFG   ARA
ESEA   AAS
.
.

# sed '/Z/d' inputfile
or 
awk '!/Z/' inputfile

awk 'END { say(_) }        
NR == 2 { l = length } 
/^>/ { 
  _ && say(_); _ = z 
  print; next 
  }
{ _ = _ ? _ $0 : $0 }
func say(x) {
    gsub(/Z/, z, x) 
    while (match(x, /........../)) {
      print substr(x, RSTART, RLENGTH)
      x = substr(x, RLENGTH + 1)
        }
    if (x) printf "%s\n\n", x
    }' infile

awk '{for(i=1; i<= NF; i++) 
         { if( match($i, /Z/)
              {next}; 
           printf("%s ", $i)}; print ""}' inputfile >newfile

$ while read line; do
> if ! echo $line | grep -o "^>.*" >/dev/null; then
> echo $line | sed 's/Z//g'
> else
> echo $line
> fi
> done <infile.dat
>tempZ_1
SAFSDAFDSG
GGERRTT
ASRARARET
WETPOASDA
ASASFAS

>temp_9
ASAEGPIOEO
EIOPIAS
FDFGARA
ESEAAAS
$

tr -d "Z\n" <infile |fold -w 10