#!/bin/bash
 
# ideone boilerplate: run in temp dir 
t=$(mktemp -d -t ideone.XXXXXXXX) || exit
trap 'rm -rf "$t"' ERR EXIT
cd "$t"
 
mkdir -p seq
 
cat <<\_ >seq/one.txt
>first sequence
aaaaaaaaa
>second_sequence
ccccccccc
_
 
cat <<\_ >seq/two.txt
>third sequence
ggggggggg
ggggggggg
> fourth sequence
tttttt
tttttt
_
 
echo "** OP's attempt"
 
awk 'BEGIN {RS=">"} {print $1}' seq/*.txt
awk 'BEGIN {RS=">"} {print toupper ($2)}' seq/*.txt
 
echo '** Solution'
 
awk '/^>/ {
  if (n) printf "\n"
  n = 0
  sub(/>[[:space:]]*/, "")
  print >>"headers.txt"
  next
}
{ printf("%s", toupper($1)); n=1 }
END { if (n) printf "\n" }' seq/*.txt >sequences.txt
 
cat headers.txt sequences.txt

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