// Load appropriate user level for this gene.
lovd_isAuthorized('gene', $sID);
lovd_requireAUTH(LEVEL_CURATOR);
require ROOT_PATH . 'class/object_genes.php';
require ROOT_PATH . 'inc-lib-form.php';
$_DATA = new LOVD_Gene();
$zData = $_DATA->loadEntry($sID);
// 2015-07-22; 3.0-14; Drop usage of CURRENT_PATH in favor of fixed $sID which may have a gene symbol with incorrect case.
// Now fix possible issues with capitalization. inc-init.php does this for $_SESSION['currdb'], but we're using $sID.
$sID = $zData['id'];
$sPath = $_PE[0] . '?' . ACTION;
if (GET) {
require ROOT_PATH . 'inc-lib-genes.php';
$aRefseqGenomic = array();
// Get LRG if it exists
if ($sLRG = lovd_getLRGbyGeneSymbol($sID)) {
$aRefseqGenomic[] = $sLRG;
}
// Get NG if it exists
if ($sNG = lovd_getNGbyGeneSymbol($sID)) {
$aRefseqGenomic[] = $sNG;
}
// Get NC from LOVD
$aRefseqGenomic[] = $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_sequences'][$zData['chromosome']];
if (!isset($_SESSION['work'][$sPath])) {
$_SESSION['work'][$sPath] = array();
}
while (count($_SESSION['work'][$sPath]) >= 5) {
unset($_SESSION['work'][$sPath][min(array_keys($_SESSION['work'][$sPath]))]);
}
// Generate an unique workID that is sortable.
}
}
$aGenesWeCanMapTo = array_unique($aGenesWeCanMapTo);
if ($aVariant['mapping_flags'] & MAPPING_ALLOW_CREATE_GENES && count($aGenesWeCanMapTo)) {
// We may add extra genes to map this variant to. $aGenes contains genes we can map to.
// Try the genes one by one.
foreach ($aGenesWeCanMapTo as $sGene) {
// Get information from HGNC.
$aGeneInfoFromHgnc = lovd_getGeneInfoFromHgncOld($sGene, array('gd_hgnc_id', 'gd_app_sym', 'gd_app_name', 'gd_pub_chrom_map', 'gd_locus_type', 'gd_pub_eg_id', 'md_mim_id', 'gd_pub_refseq_ids', 'md_refseq_id'), true);
if (empty($aGeneInfoFromHgnc)) {
// Couldn't find this gene. Try the next.
continue;
}
list($sHgncID, $sSymbol, $sGeneName, $sChromLocation, $sLocusType, $sEntrez, $sOmim, $sRefseq1, $sRefseq2) = array_values($aGeneInfoFromHgnc);
// Get LRG if it exists.
if (!($sRefseqGenomic = lovd_getLRGbyGeneSymbol($sSymbol))) {
// No LRG, get NG if it exists.
if (!($sRefseqGenomic = lovd_getNGbyGeneSymbol($sSymbol))) {
// Also no NG, use the NC instead.
$sRefseqGenomic = $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_sequences'][$sChromosome];
}
}
// Get UD.
try {
$sRefseqUD = lovd_getUDForGene($_CONF['refseq_build'], $sSymbol);
$sRef = $sRefseqUD;
} catch (SoapFault $e) {
}
// Silent error.
if (!is_string($sRefseqUD) || substr($sRefseqUD, 0, 3) != 'UD_') {
$sRefseqUD = false;
