Works with huge 1.fa file.
while (my $line =<DATA>)
$line =~ s/^\s*|\s*$//g;
if ($line =~ /^\d/)
To prevent blank lines in output caused by blank lines in 1.fa, add next unless $line =~ /\S/;
or similar after removing leading and trailing spaces.
Update: looking back this, if the ">" actually appears in the 1.fa file, then just delete it if seen while processing the line and use the above logic.