#!usr/bin/perl 
use strict;
use warnings;
if (! @ARGV) {
    print <<HELP; # Line 5
Usage:
> basecount.pl <bases file>
HELP
    exit;
} # Line 10
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 $line; # Line 15
    ++$counts{$_} for grep {/\S/} split '', $line;
}
my $bases;
my $errors;
$bases += $_ for @counts{@baseList}; # Line 20
$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; # Line 24
	# 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.Line 25
my $DNA=join('',@ARGV); my $motif=''; # Line 26
do { 
print "\n\nEnter a motif to count its number and lengths between motifs:\n";# Line 28
$motif = <STDIN>;# Line 29
# Remove the newline at the end of $motif
chomp $motif;
# Look for the motif Line 32
if ( $DNA=~ / $motif/ ) {
print "I found the motif!\n\n"; # Line 34
} else {
print"I couldn\'t find it.\n\n";
} #Line 37
# Count number of motifs and Count number of nt between two motifs 
use 5.010; # Line 39
my $string ="@ARGV";
# Remove whitespace Line 41
$string=~ s/\s//g;
my $count= () =$string=~ /$motif/g; # Line 43
print "Number of motifs: $count.\n\n";
say "The inter-motif nt Lengths are:\n"; # Line 45
say length for split/$motif/,$string;
my @a=map length,split/$motif/,$string;
# exit on an empty user input Line 48
my $output="result .txt";
unless (open(RESULT,"> $output")){
print"Cannot open file\"$output\".\n\n";# Line 51
exit;
} # Line 53
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);# Line 56
} 
until (my $motif =~ /^\s*$/ );# Line 58
exit;