Re: Seeking help for using Tie : : File in my perl program for counting bases using Active Perl 5.10.1 Build 1007

[GrandFather]

There is no need at all to use Tie anything for this task. As with many many problems that are attacked using Perl the key is to use a hash. There are bunch of newbie foibles in your code that are worth trying to clean up sooner rather than later. I haven't described the issues explicitly, but have addressed them in the following code. Have a try using the code as a starting point, and please ask about anything you don't understand:

#!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 "Total bases: $bases\n";
print join (', ', map {"$_: $counts{$_}"} @baseList), "\n";
print "Errors: $errors\n" if $errors;

Note that the code is untested and in any case I may not have understood what you are counting.