#!/usr/bin/perl –w
print "\n\nPlease type the filename: ";
$DNAfilename = <STDIN>;
chomp $DNAfilename;
# open the large file
unless ( open(DNAFILE, $DNAfilename) ) {
print "Cannot open file \"$DNAfilename\"\n\n";
exit;
} 
my @lines = <DNAFILE>; 
while (<DNAFILE>) {
  say $_;
} 
close DNAFILE;
$DNA = join( '', @lines);
# Remove whitespace
$DNA=~ s/\s//g;
# Count number of bases
$b=length($DNA);
print "\nNumber of bases: $b.";
# Count number of each base and nonbase
$A=0;$T=0;$G=0;$C=0;$e=0; 
while($DNA=~ /A/ig){$A++}
while($DNA=~ /T/ig){$T++}
while($DNA=~ /G/ig){$G++}
while($DNA=~ /C/ig){$C++}
while($DNA=~ /[^ATGC]/ig){$e++}
. . . .