Hi,
I have no problem performing such query under mysql prompt: 
mysql> SELECT Symbol FROM gene_info RIGHT JOIN gene2go ON(gene_info.`G
+eneID`= gene2go.`GeneID`) WHERE GO_Term='proteasome localization'; 
+-------------+
| Symbol      |
+-------------+
| SPBC1734.06 |
| SPBC646.09c |
| cut8        |
| rhp6        |
| SPAC1420.03 |
| SPAC3G6.02  |
| rpn5-b      |
| SPBC19C7.02 |
+-------------+
8 rows in set (2 min 19.11 sec)

[download]
But when I run this Perl script: 
use strict;
use Data::Dumper;
use Carp;
use DBI;

my $dsn = 'localhost';
my $user = 'ewijaya';
my $password = 'ewijaya';
my $dbh = DBI->connect('dbi:mysql:motif_finder','monkfan','monkpwd')
    or die "Connection Error: $DBI::errstr\n";

my $go_term = "proteasome localization";
my $sql = "SELECT Symbol FROM gene_info RIGHT JOIN gene2go ON(gene_inf
+o.`GeneID`= gene2go.`GeneID`) WHERE GO_Term=$go_term";

my  $sth = $dbh->prepare($sql);
$sth->execute or die "SQL Error: $DBI::errstr\n";


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

[download]
It gives: 
:!perl  search_gene.pl
DBD::mysql::st execute failed: You have an error in your SQL syntax; c
+heck the manual that corresponds to your MySQL server version for the
+ right syntax to use near 'localization' at line 1 at search_gene.pl 
+line 21.
SQL Error: You have an error in your SQL syntax; check the manual that
+ corresponds to your MySQL server version for the right syntax to use
+ near 'localization' at line 1

[download]
How can we correctly assign SQL command in the Perl Script?

Regards,
Edward

In reply to Problem Converting SQL term to Perl Variable by monkfan

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