function seealso_related($gene, $aa_pos, $skip_variant_id)
{
$related_variants = theDb()->getAll("SELECT v.variant_gene gene, CONCAT(v.variant_aa_from,v.variant_aa_pos,v.variant_aa_to) aa_long FROM variants v WHERE v.variant_gene=? AND v.variant_aa_pos=? AND v.variant_id <> ?", array($gene, $aa_pos, $skip_variant_id));
$seealso = "";
foreach ($related_variants as $x) {
$x["aa_short"] = aa_short_form($x["aa_long"]);
$seealso .= "<LI>See also: <A href=\"" . $x["gene"] . "-" . $x["aa_short"] . "\">" . $x["gene"] . " " . $x["aa_short"] . "</A></LI>\n";
}
if ($seealso) {
$seealso = "<DIV id=\"seealso\"><UL>{$seealso}</UL></DIV>\n";
}
return $seealso;
}
function blosum62($aa1, $aa2)
{
$aa1 = aa_short_form($aa1);
$aa2 = aa_short_form($aa2);
if ($aa1 == "X" || $aa2 == "X") {
return -10;
}
global $gBLOSUM62;
if (!is_array($gBLOSUM62["A"])) {
$keys = array_keys($gBLOSUM62);
foreach ($gBLOSUM62 as $a => &$b) {
$b = array_combine($keys, preg_split('/ ?/', $b));
array_shift($keys);
}
}
if ($aa1 <= $aa2) {
return $gBLOSUM62[$aa1][$aa2];
} else {
return $gBLOSUM62[$aa2][$aa1];
}
}
function evidence_get_variant_name(&$variant, $separator = " ", $shortp = false)
{
if (is_array($variant)) {
$row =& $variant;
} else {
if (ereg("^[0-9]+\$", $variant)) {
$row =& theDb()->getRow("SELECT * from variants WHERE variant_id=?", array($variant));
}
}
if ($row["variant_rsid"]) {
return "rs" . $row["variant_rsid"];
} else {
if ($shortp) {
return $row["variant_gene"] . $separator . aa_short_form($row["variant_aa_from"] . $row["variant_aa_pos"] . $row["variant_aa_to"]);
} else {
return $row["variant_gene"] . $separator . $row["variant_aa_from"] . $row["variant_aa_pos"] . $row["variant_aa_to"];
}
}
}
function yahoo_boss_update_external($variant_id)
{
$cache = yahoo_boss_lookup($variant_id);
if (!$cache) {
print "No search results\n";
return;
}
$variant = theDb()->getRow("SELECT v.*, vo.rsid rsid FROM variants v\n\t\t\t\t LEFT JOIN variant_occurs vo\n\t\t\t\t ON v.variant_id=vo.variant_id\n\t\t\t\t AND vo.rsid IS NOT NULL\n\t\t\t\t WHERE v.variant_id=?\n\t\t\t\t GROUP BY v.variant_id", array($variant_id));
if (!$variant || theDb()->isError($variant)) {
print "No such variant\n";
return FALSE;
}
if ($variant["variant_gene"]) {
$gene_aa_long = $variant["variant_gene"] . " " . $variant["variant_aa_from"] . $variant["variant_aa_pos"] . $variant["variant_aa_to"];
$gene_aa_short = $variant["variant_gene"] . " " . aa_short_form($variant["variant_aa_from"]) . $variant["variant_aa_pos"] . aa_short_form($variant["variant_aa_to"]);
$search_string = "{$gene_aa_long} OR {$gene_aa_short}";
if (($rsid = $variant["variant_rsid"]) || ($rsid = $variant["rsid"])) {
$search_string .= " OR rs{$rsid}";
}
} else {
$search_string = "rs" . $variant["variant_rsid"];
}
$user_url = "http://search.yahoo.com/search?p=" . urlencode($search_string);
$content = "";
$skipped_hits = 0;
if ($cache["hitcount"] > 0) {
preg_match_all('{<result>.*?</result>}is', $cache["xml"], $matches, PREG_PATTERN_ORDER);
foreach ($matches[0] as $result) {
$resulttag = array();
foreach (array("url", "dispurl", "abstract", "title") as $t) {
if (preg_match("{<{$t}>(.*?)</{$t}>}i", $result, $regs)) {
$resulttag[$t] = preg_replace('{<\\!\\[CDATA\\[(.*?)\\]\\]>}s', '$1', $regs[1]);
} else {
$resulttag = FALSE;
continue;
}
}
if (ereg("snp\\.med\\.harvard\\.edu|evidence\\.personalgenomes\\.org", $resulttag["url"])) {
$skipped_hits++;
continue;
}
if ($resulttag) {
$content .= "<LI><A href=\"" . $resulttag["url"] . "\">" . $resulttag["title"] . "</A><BR />" . $resulttag["abstract"] . "<BR /><DIV class=\"searchurl\">" . $resulttag["dispurl"] . "</DIV></LI>\n";
}
}
}
// If we skipped some hits (because they point to this page or
// Trait-o-matic), subtract them from the cached hitcount so "no
// web results except this page" gets counted as 0 for
// statistics/display.
if ($skipped_hits > 0 && preg_match('/<resultset_web\\b[^<]*\\sdeephits="?(\\d+)"?/s', $cache["xml"], $regs) && $regs[1] >= $skipped_hits) {
$hitcount = $regs[1] - $skipped_hits;
if ($hitcount != $cache["hitcount"]) {
$cache["hitcount"] = $hitcount;
theDb()->query("UPDATE yahoo_boss_cache SET hitcount=? WHERE variant_id=?", array($hitcount, $variant_id));
}
}
// Build html display for variant page
$content = "<UL><STRONG>Web search results (" . $cache["hitcount"] . " hit" . ($cache["hitcount"] == 1 ? "" : "s") . " -- <A href=\"" . $user_url . "\">see all</A>)</STRONG>" . $content . "</UL>";
theDb()->query("DELETE FROM variant_external WHERE variant_id=? AND tag=?", array($variant_id, "Yahoo!"));
$q = theDb()->query("INSERT INTO variant_external SET variant_id=?, tag=?, content=?, url=NULL, updated=NOW()", array($variant_id, "Yahoo!", $content));
}
$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}{$aa_to}");
} else {
die("Invalid variant specified");
}
}
if ($article_pmid || $genome_id || $disease_id) {
$latest_edit_id = evidence_get_latest_edit($variant_id, $article_pmid, $genome_id, $disease_id, true);
$response["latest_edit_v{$variant_id}a{$article_pmid}g{$genome_id}"] = $latest_edit_id;
$response["latest_edit_id"] = $latest_edit_id;
$renderer = new evidence_row_renderer();
$renderer->render_row(theDb()->getRow("SELECT * FROM edits WHERE edit_id=?", array($latest_edit_id)));
$response["html"] = $renderer->html();
ereg("id=\"([^\"]+)", $response["html"], $regs);
$response["e_id"] = $regs[1];
}
header("Content-type: application/json");
