Once you find the SQ line you set the flag, then you accumulate all further lines(without the spaces) into $seq untill you find a line the begins with K and only has spaces or nothing after it. Then you unset the flag.

Dumper is a nice way to printout arrays and hashes for inspection, also works with scalars too

as for your output, it will look something like

print $hash{AC}; 
print ' | ' 
print $hash{OS}; 
print ' | ' 
print $hash{OX}; 
print ' | ' 
print $hash{ID}; 
print ' | ' 
print $hash{GN}; 
print "\n"; 
my $split_after=50; 
while (length($seq)>$split_after){ 
  print substr($seq,0,50)."\n"; 
  $seq=substr($seq,$split_after);
  } 
print $seq."\n";
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Since your sample input doesnt seem to have your sample output values i cant say what the sequence of the print statements should look like. And you may need to adjust $split_after, i didnt feel like counting