From the dates in the file header, this looks like a file you've inherited. Perhaps the first thing to do is write a small script that just contains this
my @satfile = <STDIN>;
my @satseq = @satfile;
and see if it runs out of memory. If so, your datafiles are too big to read in and make a copy and you'll want to deal with one line at a time, e.g.
my $sorsz = 3;
while (my $line = <STDIN>) {
chomp $line; # to remove newlines
if ( $. <= 3 ) { # input line numbers start from 1
push @satseq, $line;
}
elsif ( $line =~ /\#/ ) {
$satseq[$sorsz] .= $line; # concatenates line onto the end
$sorsz++;
}
else{
$satseq[$sorsz] .= $line;
}
}
which is a more memory efficient way to deal with large files.
If the concatenation is still killing memory, try
substr($satseq[$sorsz],length($satseq[$sorsz]),0) = $line
Sometimes I can think of 6 impossible LDAP attributes before breakfast.
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