#!usr/bin/perl

#########################
# xmlmake_gv_full.pl
#

use DBI;

$ds = 'DBI:mysql:pageomdb;host=localhost;port=3306';
$user = 'pageom';
$pass = 'pageompassxxxx';

$string = 'rs112078';

$db = DBI->connect($ds, $user, $pass) || die "Got error $DBI::errstr when connecting to $ds\n";

# for test
$sth = $db->prepare("select * from tbl_array WHERE rsname like \'$string\%\' and subsnp_id is not null");

# real thing
#$sth = $db->prepare("select * from tbl_array WHERE subsnp_id is not null");

$sth->execute;

#print "Content-type: text/html;\n\n";
while(@row = $sth->fetchrow_array) {

# for debug

#	print "@row\n";

#	print $row[0] . "\n";
#	print $row[1] . "\n";
#	print $row[2] . "\n";

	print "\t<Genomic_Variation>\n";
	print "\t\t<id>$row[0]</id>\n";
	print "\t\t<type>SNP</type>\n";
	print "\t\t<Reference_Genome_Assembly>$row[1]</Reference_Genome_Assembly>\n";
	print "\t\t<chromosome_name>$row[2]</chromosome_name>\n";
	print "\t\t<physical_map>$row[3]</physical_map>\n";
	print "\t\t<flank_down>$row[5]</flank_down>\n";
	print "\t\t<flank_up>$row[6]</flank_up>\n";

	print "\t\t<Assayed_Genomic_Genotype>\n";
	print "\t\t\t<quality_score></quality_score>\n";
	print "\t\t\t<assay_failure>false</assay_failure>\n";
	print "\t\t\t<genotype>G/G<genotype>\n";
	print "\t\t</Assayed_Genomic_Genotype>\n";

	print "\t\t<Latent_Genotype>\n";
	print "\t\t\t<name></name>\n";
	print "\t\t\t<name></name>\n";
	print "\t\t\t<name></name>\n";

	print "\t\t\t<Genomic_Allele>\n";
	print "\t\t\t\t<name></name>\n";
	print "\t\t\t\t<name></name>\n";
	print "\t\t\t</Genomic_Allele>\n";
	print "\t\t</Latent_Genotype>\n";

	print "\t\t<Genomic_Allele_Population_Frequency>\n";
	print "\t\t\t<value></value>\n";
	print "\t\t\t<value></value>\n";
	print "\t\t</Genomic_Allele_Population_Frequency>\n";

	print "\t</Genomic_Variation>\n";

	print "\n";
}

$rc = $sth->finish;
$rc = $db->disconnect;

exit;