If you really want to prompt for input from the user after the program starts, then the advice in the first reply will take care of the immediate problem. But I would recommend using a command-line argument, which your script sees as
$ARGV[0] (you run your script via a command-line shell, don't you?)
Apart from that, you'll be better off using a placeholder in the sql query string, and passing the value to search for as a parameter when you execute the query:
#!/usr/bin/perl
use strict; # don't comment this out, and don't capitalize it.
use DBI;
my $Strain;
if ( @ARGV ) {
$Strain = shift; # get your target string from the command line
}
else {
print "Please Enter the Strain Name: ";
$Strain = <>;
chomp $Strain;
}
$dbh = DBI->connect('dbi:mysql:sampledb','root','******')
or die "Connection Error: $DBI::errstr\n";
$sql = <<EOS; # let's make it easier to read while we're at it
SELECT
feature.fastaId,
feature.contigId,
feature.orfId,
strain.strainName,
sequence.ntseq, sequence.aaseq
from feature
left join strain on feature.id=strain.id
left join sequence on feature.id=sequence.id
where strainName = ?
EOS
$sth = $dbh->prepare($sql);
$sth->execute( $Strain )
or die "SQL Error: $DBI::errstr\n";
while (@row = $sth->fetchrow_array) {
print "@row\n";
}
