Shell Programming and Scripting

>sample_1
WETYUPVLGK
DGGHHHWETY
QPERTTGGLO

>sample_2
WRRTTOOLLP
MKMKNJUTYE
DLGLTTOC
.
.

>sample_1
WETYUP
VLGKDG
GHHHWE
TYQPER
TTGGLO

>sample_2
WRRTTO
OLLPMK
MKNJUT
YEDLGL
TTOC
.
.

$ ruby -00 -ne 'f=$_.split("\n");f[1..-1]=f[1..-1].join.scan(/.{6}/);f[-1]<<"\n\n";print f.join("\n")' file
>sample_1
WETYUP
VLGKDG
GHHHWE
TYQPER
TTGGLO

>sample_2
WRRTTO
OLLPMK
MKNJUT
YEDLGL

awk '/>/||/^$/ {print;next} {printf $0}' infile |awk  'BEGIN{FS=OFS=""}! />/ {for (i=1;i<=int(NF/6);i++) $(i*6)=$(i*6) RS}1'

awk '{printf("%s%s\n",r,$1);r=ORS;$1=""} {
  for (i=1;i<=length;i+=6) {
    print substr($0,i,6)
  }
}' RS= OFS= file

$
$
$ cat f22
WETYUPVLGK
DGGHHHWETY
QPERTTGGLO
WRRTTOOLLP
MKMKNJUTYE
DLGLTTOCXX
$
$ perl -lne '$x.=$_; do{print substr($x,0,6); $x=substr($x,6)} until(length $x<6)' f22
WETYUP
VLGKDG
GHHHWE
TYQPER
TTGGLO
WRRTTO
OLLPMK
MKNJUT
YEDLGL
TTOCXX
$
$

tr -d \\\n <file | sed 's/\(.\{6\}\)/&\
/g'

sed -n '/>/{p;n;N;N;s/\n//g;s/....../&\n/gp}' infile