#!/usr/bin/perl

use strict;
use DBI;
use vars qw ( $opt_h $opt_m $opt_o $opt_i );
use Getopt::Std;

getopts('hi:o:m:');

print "You forgot to remove the exit statement at the top of the program\n";
exit;

if($opt_h) {
    print <<HELP;

program_name.pl: HERE IS THE PROGRAM DESCRIPTION

Usage:

   perl program_name.pl -i <input file> -o <output file> -m <"dbname|host|user|pwd">

Arguments:
   -h  displays this help message
   -i  input file (required)
   -o  output file (required)
   -m  MySQL login information in the form "dbname|host|user|password" (required)

HELP
exit;
}

my $errstring = "";

my ($dbname,$host,$user,$pwd);
if($opt_m) {
    ($dbname,$host,$user,$pwd) = split(/\|/,$opt_m);
    if($dbname eq "" || $host eq "" || $user eq "" || $pwd eq "") {
        $errstring .= "You must supply complete MySQL login information (-m).\n";
    }
} else {
    $errstring .= "You must supply the MySQL login information (-m).\n";
}

my $input_file;
if($opt_i) {
    $input_file = $opt_i;
} else {
    $errstring .= "Input file required (-i).\n";
}

my $output_file;
if($opt_o) {
    $output_file = $opt_o;
} else {
    $errstring .= "Output file required (-o).\n";
}

if($errstring ne "") {
    #there is commandline info missing
    print "ERROR - Missing information on the commandline (use -h for help):\n$errstring";
    exit;
}

############################################

my (@row);

############## DATABASE CODE

my $dbh = DBI->connect("DBI:mysql:$dbname:$host",$user,$pwd)
   or die "Can't connect to database!\n";

my $query = "show tables";

my $sth = $dbh->prepare($query) or die "Can't prepare $query: " . $dbh->errstr . "\n";
$sth->execute or die "Can't execute query: " . $dbh->errstr . "\n";

while(@row = $sth->fetchrow_array) {
    print "@row\n";
}

$dbh->disconnect;


############## TAB DELIMTED (TSV) TEXT CODE

open(FILE,$input_file);
open(OUT,">$output_file");
while(<FILE>) {
    chomp;
    @row = split(/\t/);

    print "@row\n";
}
close(OUT);
close(FILE);


##############

exit(0);