#!usr/bin/perl 
use strict;
use warnings;
if (! @ARGV) {
    print <<HELP; 
Usage:
> basecount.pl <bases file>
HELP
    exit;
} open my $dnaIn, '<', $ARGV[0] or die "Can't open bases file $ARGV[0]: +$!\n";
my %counts;
my @baseList = qw(A T G C);
while (defined (my $line = <$dnaIn>)) {
    chomp $line; 
    ++$counts{$_} for grep {/\S/} split '', $line;
}
my $bases;
my $errors;
$bases += $_ for @counts{@baseList}; 
$errors += $_ for map {$counts{$_}} grep {! /[ATGC]/} keys %counts;
print "\n\n Total bases: $bases\n\n";
print join (', ', map {"$_= $counts{$_}"} @baseList), "\n";
print "Errors (N)= $errors\n" if $errors; 

# In a loop, ask the user for a motif, search for the motif, and report if it # was found. Exit if no motif is entered. 
my $DNA=join('',@ARGV); my $motif=''; do { 
print "\n\nEnter a motif to count its number and lengths between motifs:\n";# $motif = <STDIN>;
chomp $motif;

# Look for the motif 
if ( $DNA=~ / $motif/ ) {
print "I found the motif!\n\n"; 
} else {
print"I couldn\'t find it.\n\n";
} 
# Count number of motifs and Count number of nt between two motifs 
use 5.010; 
my $string ="@ARGV";
# Remove whitespace 
$string=~ s/\s//g;
my $count= () =$string=~ /$motif/g; 
  print "Number of motifs: $count.\n\n";
say "The inter-motif nt Lengths are:\n"; 
say length for split/$motif/,$string;
my @a=map length,split/$motif/,$string;

# Output to a text page
my $output="result .txt";
unless (open(RESULT,"> $output")){
print"Cannot open file\"$output\".\n\n";
exit;
} 
print RESULT"\n\n Number of bases: $bases.  Errors(N)=$errors.\n
  Motif: $motif. Number of motifs: $count.\n\n The inter-motif nt Lengths      are:\n\n    @a";
close(RESULT);
} 
until (my $motif =~ /^\s*$/ );
exit;