#!/usr/bin/perl -w
use strict;
use DBI;
use CGI;
use CGI::Carp('fatalsToBrowser');
my $query = new CGI;
print $query->header();
my $my_database = "TrypSnoDB";
my $localhost = "localhost";
my $dsn = "DBI:mysql:$my_database:$localhost";
my $db_user_name = "adrian";
my $db_password = "temp_pass";
my $dbh = DBI->connect("DBI:mysql:database=TrypSnoDB;host=localhost;mysql_socket=/private/software/mysql/mysql.sock","adrian","temp_pass", {'RaiseError' => 1});
print "\n";
print "\n";
print "Welcome to the T. Brucei snoRNA Database\n";
print "\n";
print "\n";
print "\n";
print "
Trypanosomatid snoRNA Database
\n";
print "\n";
print "\n";
print "\n";
if ($query->param('submit1')){
my $orig_sno = $query->param('snorna1');
my $family = $query->param('family1');
my $query_type = $query->param('target_option1');
my $target = $query->param('target_name1');
if ($orig_sno eq "Trypanosoma brucei") {
$orig_sno = 1;
}
elsif ($orig_sno eq "Leishmania major") {
$orig_sno = 7;
}
elsif ($orig_sno eq "ALL") {
$orig_sno = "1 or ST.org_id=7";
}
if ($family eq "ALL") {
$family = "'C/D' or ST.family='H/ACA'";
}
else {
$family = "'$family'";
}
if ($target ne "ALL") {
$family = "$family and T.target_name='$target'";
}
my($db_query,$common_tar,$exp_ver_sno,$exp_ver_tar,$total);
$db_query = "SELECT ST.sno_name,T.target_name,T.location,T.base_pair,SM.annotated_seq FROM sno_Table ST,sno_Modifications SM,Targets T WHERE ST.sno_id=SM.sno_id and SM.mod_id=T.target_id and (ST.org_id=$orig_sno) and (ST.family=$family)";
$common_tar="and T.target_id in(SELECT T.target_id FROM sno_Table ST,sno_Modifications SM,Targets T WHERE ST.sno_id=SM.sno_id and SM.mod_id=T.target_id group by T.target_id having count(*)=2) order by T.location desc";
$exp_ver_sno="and ST.exper_ver='Y'";
$exp_ver_tar = "and T.exp_ver='Y'";
if ($query_type eq "snoRNAs with common targets") {
$db_query=$db_query.$common_tar;
}
elsif ($query_type eq "Experimentally verified snoRNAs") {
$db_query=$db_query.$exp_ver_sno;
}
elsif ($query_type eq "snoRNAs with experimentally verified targets") {
$db_query=$db_query.$exp_ver_tar;
}
elsif ($query_type eq "ALL"){
$db_query=$db_query;
}
my $sth = $dbh->prepare($db_query);
$sth->execute();
my$total = $sth->rows;
print "
\n";
print "\n";
print "\n";
if ($query->param('submit1')){
my $orig_sno = $query->param('snorna1');
my $family = $query->param('family1');
my $query_type = $query->param('target_option1');
my $target = $query->param('target_name1');
if ($orig_sno eq "Trypanosoma brucei") {
$orig_sno = 1;
}
elsif ($orig_sno eq "Leishmania major") {
$orig_sno = 7;
}
elsif ($orig_sno eq "ALL") {
$orig_sno = "1 or ST.org_id=7";
}
if ($family eq "ALL") {
$family = "'C/D' or ST.family='H/ACA'";
}
else {
$family = "'$family'";
}
if ($target ne "ALL") {
$family = "$family and T.target_name='$target'";
}
my($db_query,$common_tar,$exp_ver_sno,$exp_ver_tar,$total);
$db_query = "SELECT ST.sno_name,T.target_name,T.location,T.base_pair,SM.annotated_seq FROM sno_Table ST,sno_Modifications SM,Targets T WHERE ST.sno_id=SM.sno_id and SM.mod_id=T.target_id and (ST.org_id=$orig_sno) and (ST.family=$family)";
$common_tar="and T.target_id in(SELECT T.target_id FROM sno_Table ST,sno_Modifications SM,Targets T WHERE ST.sno_id=SM.sno_id and SM.mod_id=T.target_id group by T.target_id having count(*)=2) order by T.location desc";
$exp_ver_sno="and ST.exper_ver='Y'";
$exp_ver_tar = "and T.exp_ver='Y'";
if ($query_type eq "snoRNAs with common targets") {
$db_query=$db_query.$common_tar;
}
elsif ($query_type eq "Experimentally verified snoRNAs") {
$db_query=$db_query.$exp_ver_sno;
}
elsif ($query_type eq "snoRNAs with experimentally verified targets") {
$db_query=$db_query.$exp_ver_tar;
}
elsif ($query_type eq "ALL"){
$db_query=$db_query;
}
my $sth = $dbh->prepare($db_query);
$sth->execute();
my$total = $sth->rows;
print "