function evidence_get_variant_id($gene, $aa_pos = false, $aa_from = false, $aa_to = false, $create_flag = false)
{
if ($aa_pos === false && ereg('^rs([0-9]+)$', $gene, $regs)) {
// Return the gene/AA variant if one is already known to be caused
// by this rsid
$variant_id = theDb()->getOne("SELECT v.variant_id\n\t\t\t\t FROM variant_occurs vo\n\t\t\t\t LEFT JOIN variants v\n\t\t\t\t ON v.variant_id = vo.variant_id\n\t\t\t\t WHERE vo.rsid=?\n\t\t\t\t AND v.variant_rsid IS NULL\n\t\t\t\t AND v.variant_id IS NOT NULL\n\t\t\t\t LIMIT 1", array($regs[1]));
if (theDb()->isError($variant_id)) {
die($variant_id->getMessage());
}
if ($variant_id) {
return $variant_id;
}
if ($create_flag) {
$q = theDb()->query("INSERT IGNORE INTO variants\n\t\t\t SET variant_rsid=?", array($regs[1]));
if (!theDb()->isError($q) && theDb()->affectedRows()) {
return theDb()->getOne("SELECT LAST_INSERT_ID()");
}
}
return theDb()->getOne("SELECT variant_id FROM variants\n\t\t\t\tWHERE variant_rsid=?", array($regs[1]));
}
if ($aa_pos === false) {
if (ereg("^([-A-Za-z0-9_]+)[- ]+([A-Za-z]+)([0-9]+)([A-Za-z\\*]+)\$", $gene, $regs)) {
$gene = $regs[1];
$aa_from = $regs[2];
$aa_pos = $regs[3];
$aa_to = $regs[4];
} else {
return null;
}
} else {
if (!aa_sane("{$aa_from}{$aa_pos}{$aa_to}")) {
return null;
}
}
$gene = strtoupper($gene);
$aa_from = aa_long_form($aa_from);
$aa_to = aa_long_form($aa_to);
if ($create_flag) {
$official_gene = theDb()->getOne("SELECT official FROM gene_canonical_name WHERE aka=?", array($gene));
if (!theDb()->isError($official_gene) && strlen($official_gene) && !theDb()->getOne("SELECT 1 FROM variants WHERE variant_gene=? AND variant_aa_pos=? AND variant_aa_from=? AND variant_iaa_to=?", array($gene, $aa_pos, $aa_from, $aa_to))) {
$gene = $official_gene;
}
$q = theDb()->query("INSERT IGNORE INTO variants\n\t\t\tSET variant_gene=?,\n\t\t\tvariant_aa_pos=?,\n\t\t\tvariant_aa_from=?,\n\t\t\tvariant_aa_to=?", array($gene, $aa_pos, $aa_from, $aa_to));
if (!theDb()->isError($q) && theDb()->affectedRows()) {
return theDb()->getOne("SELECT LAST_INSERT_ID()");
}
}
return theDb()->getOne("SELECT variant_id FROM variants\n\t\t\t\tWHERE variant_gene=?\n\t\t\t\tAND variant_aa_pos=?\n\t\t\t\tAND variant_aa_from=?\n\t\t\t\tAND variant_aa_to=?", array($gene, $aa_pos, $aa_from, $aa_to));
}
$q = theDb()->query("ALTER TABLE counsyl_a\n ADD aa_pos INT,\n ADD aa_from CHAR(4),\n ADD aa_to CHAR(4)");
if (theDb()->isError($q)) {
print $q->getMessage();
}
$q = theDb()->query("UPDATE counsyl_a\n SET aa_pos=SUBSTR(aa_change,2,LENGTH(aa_change)-2),\n aa_from=SUBSTR(aa_change,1,1),\n aa_to=SUBSTR(aa_change,LENGTH(aa_change),1)");
if (theDb()->isError($q)) {
print $q->getMessage();
}
print theDb()->affectedRows();
print "\n";
print "Translating AA to 3-letter symbols...";
foreach (array_keys($aa_13) as $aa) {
theDb()->query("UPDATE counsyl_a SET aa_from=? WHERE aa_from=?", array(aa_long_form($aa), $aa));
print theDb()->affectedRows();
print ",";
theDb()->query("UPDATE counsyl_a SET aa_to=? WHERE aa_to=?", array(aa_long_form($aa), $aa));
print theDb()->affectedRows();
print ",";
}
print "\n";
print "Deleting bogus rows...";
$q = theDb()->query("DELETE FROM counsyl_a WHERE aa_pos=0 OR LENGTH(aa_from)<3 OR LENGTH(aa_to)<3");
if (theDb()->isError($q)) {
print $q->getMessage();
}
print theDb()->affectedRows();
print "\n";
print "Looking up gene,aa -> variant_id...";
theDb()->query("ALTER TABLE counsyl_a ADD variant_id BIGINT UNSIGNED, ADD INDEX(variant_id)");
$q = theDb()->query("UPDATE counsyl_a c\n LEFT JOIN variants v\n ON v.variant_gene=c.gene\n AND v.variant_aa_from=c.aa_from\n AND v.variant_aa_pos=c.aa_pos\n AND v.variant_aa_to=c.aa_to\n set c.variant_id=v.variant_id");
print theDb()->affectedRows();
$variant_name = evidence_get_variant_name($variant_id, "-", true);
if ($regs[1] != $variant_name) {
header("Location: {$variant_name}");
exit;
}
$max_edit_id = $regs[3];
} else {
if (ereg("^([A-Za-z0-9_-]+)[- \t\n]+([A-Za-z]+[0-9]+[A-Za-z\\*]+)(;([0-9]+))?\$", $_GET["q"], $regs) && aa_sane($aa = $regs[2])) {
$gene = strtoupper($regs[1]);
$max_edit_id = $regs[4];
$variant_id = evidence_get_variant_id($variant_name = "{$gene} {$aa}");
}
}
}
if (!$variant_id && $aa) {
$aa_long = aa_long_form($aa);
$aa_short = aa_short_form($aa_long);
header("HTTP/1.1 404 Not found");
$gOut["title"] = "{$gene} {$aa_short}";
$gOut["content"] = <<<EOF
<H1>{$gene} {$aa_short}</H1>
<P>({$gene} {$aa_long})</P>
<P>There is no GET-Evidence entry for this variant.</P>
EOF;
if (ereg("[0-9]+", $aa, $regs)) {
$gOut["content"] .= seealso_related($gene, $regs[0], 0);
}
if (getCurrentUser()) {
}
if (ereg("^[0-9]+\$", $_POST["genome_id"], $regs)) {
$genome_id = $regs[0];
} else {
$genome_id = 0;
}
if (ereg("^[0-9]+\$", $_POST["disease_id"], $regs)) {
$disease_id = $regs[0];
} else {
$disease_id = 0;
}
if (ereg("^[0-9]+\$", $_POST["variant_id"], $regs)) {
$variant_id = $regs[0];
} else {
if (aa_sane($_POST["variant_aa_change"])) {
if (ereg("^([^0-9]+)([0-9]+)([^0-9]+)\$", aa_long_form($_POST["variant_aa_change"]), $regs)) {
$aa_from = $regs[1];
$aa_pos = $regs[2];
$aa_to = $regs[3];
}
$gene = strtoupper($_POST["variant_gene"]);
$variant_id = evidence_get_variant_id($gene, $aa_pos, $aa_from, $aa_to, true);
$edit_id = evidence_get_latest_edit($variant_id, 0, 0, 0, true);
$response["latest_edit_v{$variant_id}a0g0"] = $edit_id;
$response["latest_edit_id"] = $edit_id;
$response["variant_id"] = $variant_id;
$response["please_reload"] = true;
$response["variant_key"] = "{$gene} " . aa_short_form("{$aa_from}{$aa_pos}{$aa_to}");
} else {
die("Invalid variant specified");
}
