Exemple #1
0
    return $seealso;
}
$_GET["q"] = trim($_GET["q"], "\" \t\n\r");
if (ereg("^[0-9]+\$", $_GET["q"])) {
    $variant_id = $_GET["q"];
} else {
    if (ereg("^(rs[0-9]+)(;([0-9]+))?\$", $_GET["q"], $regs)) {
        $variant_id = evidence_get_variant_id($regs[1]);
        $variant_name = evidence_get_variant_name($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>
Exemple #2
0
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));
}
Exemple #3
0
     $article_pmid = 0;
 }
 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");