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functions.php
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<?php
require_once("config.php");
require_once("db_connection.php");
$clinicalSignificanceMapping = [
'Benign' => ["Benign", "Benign, association", "Benign/Likely benign", "Benign/Likely benign, Affects", "Benign/Likely benign, association", "Benign/Likely benign, drug response", "Benign/Likely benign, drug response, risk factor", "Benign/Likely benign, other", "Benign/Likely benign, protective", "Benign/Likely benign, protective, risk factor", "Benign/Likely benign, risk factor", "Benign, other", "Benign, risk factor", "Likely benign", "Likely benign, drug response, other", "Likely benign, other", "Likely benign, risk factor"],
'Pathogenic' => ["Pathogenic", "Pathogenic, Affects", "Pathogenic, association, protective", "Pathogenic, drug response", "Pathogenic/Likely pathogenic", "Pathogenic/Likely pathogenic, drug response", "Pathogenic/Likely pathogenic, other", "Pathogenic/Likely pathogenic, risk factor", "Pathogenic, other", "Pathogenic, other, risk factor", "Pathogenic, protective", "Pathogenic, risk factor", "Likely pathogenic", "Likely pathogenic, association", "Likely pathogenic, drug response", "Likely pathogenic, other", "Likely pathogenic, risk factor"],
'VUS' => ["Uncertain significance", "Uncertain significance, drug response", "Uncertain significance, other", "Uncertain significance, risk factor"],
'Conflicting' => ["conflicting data from submitters", "Conflicting interpretations of pathogenicity", "Conflicting interpretations of pathogenicity, Affects", "Conflicting interpretations of pathogenicity, Affects, association, drug response, other", "Conflicting interpretations of pathogenicity, Affects, association, risk factor", "Conflicting interpretations of pathogenicity, Affects, other", "Conflicting interpretations of pathogenicity, association", "Conflicting interpretations of pathogenicity, association, other, risk factor", "Conflicting interpretations of pathogenicity, drug response", "Conflicting interpretations of pathogenicity, other", "Conflicting interpretations of pathogenicity, other, risk factor", "Conflicting interpretations of pathogenicity, protective", "Conflicting interpretations of pathogenicity, risk factor"],
'Others' => ["drug response", "drug response, protective, risk factor", "drug response, risk factor", "no interpretation for the single variant", "not provided", "other", "Affects", "Affects, association", "Affects, risk factor", "association", "association, protective", "association, risk factor", "protective", "protective, risk factor", "risk factor"]
];
$disease_cat_mapping = ['C01' => 'Bacterial Infections and Mycoses ', 'C02' => 'Virus Diseases ', 'C03' => 'Parasitic Diseases ', 'C04' => 'Neoplasms ', 'C05' => 'Musculoskeletal Diseases ', 'C06' => 'Digestive System Diseases ', 'C07' => 'Stomatognathic Diseases ', 'C08' => 'Respiratory Tract Diseases ', 'C09' => 'Otorhinolaryngologic Diseases ', 'C10' => 'Nervous System Diseases ', 'C11' => 'Eye Diseases ', 'C12' => 'Male Urogenital Diseases ', 'C13' => 'Female Urogenital Diseases and Pregnancy Complications ', 'C14' => 'Cardiovascular Diseases ', 'C15' => 'Hemic and Lymphatic Diseases ', 'C16' => 'Congenital, Hereditary, and Neonatal Diseases and Abnormalities ', 'C17' => 'Skin and Connective Tissue Diseases ', 'C18' => 'Nutritional and Metabolic Diseases ', 'C19' => 'Endocrine System Diseases ', 'C20' => 'Immune System Diseases ', 'C21' => 'Disorders of Environmental Origin ', 'C22' => 'Animal Diseases ', 'C23' => 'Pathological Conditions, Signs and Symptoms ', 'C24' => 'Occupational Diseases ', 'C25' => 'Chemically-Induced Disorders ', 'C26' => 'Wounds and Injuries ', 'F01' => 'Behavior and Behavior Mechanisms ', 'F02' => 'Psychological Phenomena ', 'F03' => 'Mental Disorders '];
function arrayFind($needle, $haystack)
{
foreach ($haystack as $key => $item) {
if (@strpos($item, $needle) !== FALSE) {
return $key;
break;
}
}
}
$availableSpecies = ["human", "chimp", "macaque", "rat", "mouse", "zebrafish", "frog", "fruitfly", "worm", "yeast"];
function getHumanHomolog($geneId)
{
if ($geneId == null) {
return false;
}
global $db_connection;
$availableSpecies = ["human", "chimp", "macaque", "rat", "mouse", "zebrafish", "frog", "fruitfly", "worm", "yeast"];
$geneId = str_replace('"', '', $geneId);
for ($i = 0; $i < count($availableSpecies); $i++) {
$availableSpecies[$i] = "FIND_IN_SET('{$geneId}', {$availableSpecies[$i]}_gene_id)";
}
$geneInfoHuman = mysqli_query(
$db_connection,
"SELECT homology.*, symb.meta_value as human_gene_symbol FROM homology
JOIN ncbi_gene_meta symb ON symb.ncbi_gene_id = homology.human_gene_id
and symb.meta_key = 'gene_symbol'
WHERE " . implode(' or ', $availableSpecies)
);
if (mysqli_num_rows($geneInfoHuman) == 0) {
return null;
}
$homology = mysqli_fetch_assoc($geneInfoHuman);
$speciesName = str_replace('_gene_id', '', arrayFind($geneId, $homology));
return [
'human_gene_id' => $homology['human_gene_id'],
'species_name' => $speciesName,
'gene_id' => $geneId,
'human_gene_symbol' => $homology['human_gene_symbol']
];
}
function processMSA($row)
{
$fasta = $row['fasta'];
$fasta = explode("\n>", trim($fasta));
$homo = @end(array_filter($fasta, function ($x) {
return strpos($x, 'Homo sapiens') !== false;
}));
$mouse = @end(array_filter($fasta, function ($x) {
return strpos($x, 'Mus musculus') !== false;
}));
$worm = @end(array_filter($fasta, function ($x) {
return strpos($x, 'Caenorhabditis elegans') !== false;
}));
$homoId = array_search($homo, $fasta);
$mouseId = array_search($mouse, $fasta);
$wormId = array_search($worm, $fasta);
if ($homoId != 0) {
$fasta[$homoId] = $fasta[0];
$fasta[0] = $homo;
}
if ($mouseId != 0) {
$fasta[$mouseId] = $fasta[1];
$fasta[1] = $mouse;
}
if ($wormId != 0) {
$fasta[$wormId] = $fasta[2];
$fasta[2] = $worm;
}
$fasta = '>' . trim(implode("\n>", $fasta));
$fasta = preg_replace('@>{2,}@', '>', $fasta);
preg_match('@^(.*?) @', $homo, $npId);
preg_match('@^(.*?) @', $mouse, $npMouseId);
preg_match('@^(.*?) @', $worm, $npWormId);
$npId = $npId[1];
$npMouseId = $npMouseId[1];
$npWormId = $npWormId[1];
$transcriptId = str_replace('>', '', trim($npId));
$transcriptMouseId = str_replace('>', '', trim($npMouseId));
$transcriptWormId = str_replace('>', '', trim($npWormId));
return [
'id' => $row['id'], 'fasta' => $fasta, 'human_transcript_id' => $transcriptId,
'human_convart_gene_id' => getConvartGeneIdByDbId($transcriptId), 'mouse_transcript_id' => $transcriptMouseId, 'worm_transcript_id' => $transcriptWormId
];
}
function getConvartGeneIdByDbId($transcriptId)
{
global $db_connection;
$transcriptId = explode('.', $transcriptId)[0];
$query = mysqli_query($db_connection, "SELECT convart_gene_id FROM convart_gene_to_db WHERE db_id='$transcriptId'");
$row = mysqli_fetch_assoc($query);
return $row['convart_gene_id'];
}
function getTranscriptIdByConvartGeneId($convartGeneId)
{
global $db_connection;
$query = mysqli_query($db_connection, "SELECT db_id FROM convart_gene_to_db WHERE convart_gene_id ='$convartGeneId' LIMIT 1");
$row = mysqli_fetch_assoc($query);
return $row['db_id'];
}
function getProteinIdByConvartGeneIdMouse($convartGeneId)
{
global $db_connection;
$query = mysqli_query($db_connection, "SELECT db_id FROM convart_gene_to_db WHERE convart_gene_id ='$convartGeneId' AND db = 'NP' LIMIT 1");
$row = mysqli_fetch_assoc($query);
return $row['db_id'];
}
function getMSAByGeneId($convartGeneId, $withFasta = true)
{
global $db_connection;
$withoutVersion = explode('.', $convartGeneId)[0];
if ($withFasta) {
$query = mysqli_query($db_connection, "SELECT id, fasta FROM msa AS m INNER JOIN msa_gene AS mg ON " .
"mg.msa_id = m.id INNER JOIN convart_gene_to_db as gdb ON gdb.convart_gene_id=mg.convart_gene_id " .
"INNER JOIN msa_best_combination as mb ON m.id=mb.msa_id WHERE " .
"(gdb.db_id='{$withoutVersion}')
LIMIT 1");
if (mysqli_num_rows($query) == 0) {
#Burayı 19.11.2020'de msa_best_combination tablosunda bulunmayan genler için yazdım. (Ahmet Sayıcı)
#return null;
$query = mysqli_query($db_connection, "SELECT mg.msa_id AS id, mg_hum.convart_gene_id AS human_convart_gene_id,
ncbi_hum.ncbi_gene_id AS ncbi_gene_id
FROM msa_gene AS mg " .
" INNER JOIN msa_gene AS mg_hum ON mg_hum.msa_id = mg.msa_id
LEFT JOIN convart_gene_to_db as gdb ON gdb.convart_gene_id=mg.convart_gene_id
INNER JOIN ncbi_gene_meta AS ncbi_hum ON
ncbi_hum.meta_value='{$withoutVersion}'
WHERE " .
"
(gdb.db_id='{$withoutVersion}')
LIMIT 1");
if (mysqli_num_rows($query) == 0) {
#Burayı 19.11.2020'de msa_best_combination tablosunda bulunmayan genler için yazdım. (Ahmet Sayıcı)
return null;
}
$row = mysqli_fetch_assoc($query);
return $row;
}
$row = mysqli_fetch_assoc($query);
return processMSA($row);
} else {
$query = mysqli_query($db_connection, "SELECT mg.msa_id AS id, mg_hum.convart_gene_id AS human_convart_gene_id,
ncbi_hum.ncbi_gene_id AS ncbi_gene_id
FROM msa_gene AS mg " .
" INNER JOIN msa_gene AS mg_hum ON mg_hum.msa_id = mg.msa_id
INNER JOIN msa_best_combination AS mb ON mg_hum.convart_gene_id=mb.convart_gene_id
LEFT JOIN convart_gene_to_db as gdb ON gdb.convart_gene_id=mg.convart_gene_id
INNER JOIN ncbi_gene_meta AS ncbi_hum ON
ncbi_hum.meta_value='{$withoutVersion}'
WHERE " .
"
(gdb.db_id='{$withoutVersion}')
LIMIT 1");
echo mysqli_error($db_connection);
if (mysqli_num_rows($query) == 0) {
#Burayı 19.11.2020'de msa_best_combination tablosunda bulunmayan genler için yazdım. (Ahmet Sayıcı)
#return null;
$query = mysqli_query($db_connection, "SELECT mg.msa_id AS id, mg_hum.convart_gene_id AS human_convart_gene_id,
ncbi_hum.ncbi_gene_id AS ncbi_gene_id
FROM msa_gene AS mg " .
" INNER JOIN msa_gene AS mg_hum ON mg_hum.msa_id = mg.msa_id
LEFT JOIN convart_gene_to_db as gdb ON gdb.convart_gene_id=mg.convart_gene_id
INNER JOIN ncbi_gene_meta AS ncbi_hum ON
ncbi_hum.meta_value='{$withoutVersion}'
WHERE " .
"
(gdb.db_id='{$withoutVersion}')
LIMIT 1");
if (mysqli_num_rows($query) == 0) {
#Burayı 19.11.2020'de msa_best_combination tablosunda bulunmayan genler için yazdım. (Ahmet Sayıcı)
return null;
}
$row = mysqli_fetch_assoc($query);
#echo $row;
return $row;
}
$row = mysqli_fetch_assoc($query);
return $row;
}
}
function hasMSA($convartGeneId)
{
global $db_connection;
$convartGeneIdWithoutVersion = explode('.', $convartGeneId)[0];
$query = mysqli_query($db_connection, "SELECT msa_id FROM msa_gene AS mg LEFT JOIN convart_gene_to_db as gdb ON
gdb.convart_gene_id=mg.convart_gene_id WHERE
mg.convart_gene_id='{$convartGeneId}' OR gdb.db_id='{$convartGeneIdWithoutVersion}'");
return mysqli_num_rows($query) > 0;
}
function getMSAById($id)
{
global $db_connection;
$query = mysqli_query($db_connection, "SELECT id, fasta FROM msa AS m WHERE m.id='{$id}' LIMIT 1");
if (mysqli_num_rows($query) == 0) {
return null;
}
$row = mysqli_fetch_assoc($query);
return processMSA($row);
}
function getGeneDetailsByENSTIdFromAPI(&$geneDetails, $transcriptId)
{
$transcriptId = explode('.', $transcriptId)[0];
$rawData = file_get_contents('https://rest.ensembl.org/lookup/id/' . $transcriptId . '?content-type=application/json;expand=0');
$data = json_decode($rawData);
$geneDetails['gene_symbol'] = $data->display_name;
$geneDetails['gene_synonym'] = $data->display_name;
$geneDetails['protein_number'] = $transcriptId;
$geneDetails['ENSG'] = $data->Parent;
//return $geneDetails;
}
function getNCBIDetailsById($geneId)
{
global $db_connection;
$geneIdNoVersion = explode('.', $geneId)[0];
$query = mysqli_query($db_connection, "SELECT nc0.ncbi_gene_id AS gene_id, nc0.meta_key, GROUP_CONCAT(nc0.meta_value) AS meta_value FROM ncbi_gene_meta AS nc0 INNER JOIN ncbi_gene_meta AS nc1 ON (nc1.ncbi_gene_id='{$geneId}' OR nc1.meta_value='{$geneId}' OR nc1.meta_value='{$geneIdNoVersion}' ) WHERE nc0.ncbi_gene_id=nc1.ncbi_gene_id GROUP BY meta_key");
$details = [];
$details['dbs'] = [];
$details['dbs']['ENST'] = [];
while ($row = @mysqli_fetch_assoc($query)) {
$values = explode(',', $row['meta_value']);
$uniqueValues = array_unique($values);
$details[$row['meta_key']] = implode(',', $uniqueValues);
$details['dbs']['NCBI'] = $row['gene_id'];
}
if (strstr($geneId, 'ENST')) {
$details['dbs']['ENST'][] = explode('.', $geneId)[0];
}
return $details;
}
function getGeneDetailsById($geneId, $withSequence = false)
{
global $db_connection;
global $availableSpecies;
if (empty($geneId)) {
return null;
}
$geneIdNoVersion = explode('.', $geneId)[0];
$details = getNCBIDetailsById($geneId);
$query = mysqli_query($db_connection, "SELECT cg2.convart_gene_id, cg2.db, cg2.db_id FROM convart_gene_to_db AS cg1 " .
"INNER JOIN convart_gene_to_db AS cg2 ON cg2.convart_gene_id=cg1.convart_gene_id " .
"WHERE cg1.db_id='{$geneId}' or cg1.db_id='{$geneIdNoVersion}'");
while ($db = mysqli_fetch_assoc($query)) {
$details['convart_gene_id'] = $db['convart_gene_id'];
$details['dbs'][$db['db']][] = explode('.', $db['db_id'])[0];
}
foreach ($details['dbs'] as $db => $ids) {
if (!is_array($details['dbs'][$db])) {
$details['dbs'][$db] = [$details['dbs'][$db]];
}
$details['dbs'][$db] = '"' . implode('","', array_unique($details['dbs'][$db])) . '"';
}
if (isset($details['dbs']['ENST'])) {
$details['ENST'] = $details['dbs']['ENST'];
}
if ($withSequence) {
$query = mysqli_query($db_connection, "SELECT sequence FROM convart_gene WHERE id='{$details['convart_gene_id']}'");
$row = mysqli_fetch_assoc($query);
$details['sequence'] = $row['sequence'];
}
return $details;
}
function createMSA($fasta, $ids, $alignment_method)
{
global $db_connection;
if ($stmt = mysqli_prepare($db_connection, "INSERT INTO msa (fasta, alignment_method) VALUES(?, ?)")) {
mysqli_stmt_bind_param($stmt, "ss", $fasta, $alignment_method);
mysqli_stmt_execute($stmt);
}
$msaId = mysqli_insert_id($db_connection);
foreach ($ids as $id) {
mysqli_query($db_connection, "INSERT INTO msa_gene (msa_id, convart_gene_id) VALUES({$msaId}, {$id})");
}
if (mysqli_error($db_connection)) {
echo mysqli_error($db_connection);
exit;
}
return $msaId;
}
function getGeneDetailsByConvartId($convartGeneId, $ncbiGeneId)
{
global $db_connection;
global $availableSpecies;
$details = getNCBIDetailsById($ncbiGeneId);
$details['dbs']['NCBI'] = [$ncbiGeneId];
$query = mysqli_query($db_connection, "SELECT cg2.db, cg2.db_id FROM convart_gene_to_db AS cg1 " .
"INNER JOIN convart_gene_to_db AS cg2 ON cg2.convart_gene_id=cg1.convart_gene_id " .
"WHERE cg1.convart_gene_id='{$convartGeneId}'");
while ($db = mysqli_fetch_assoc($query)) {
$details['dbs'][$db['db']][] = explode('.', $db['db_id'])[0];
}
foreach ($details['dbs'] as $db => $ids) {
$details['dbs'][$db] = '"' . implode('","', array_unique($details['dbs'][$db])) . '"';
}
if (isset($details['dbs']['ENST'])) {
$details['ENST'] = $details['dbs']['ENST'];
}
return $details;
}
function getHumanProteinDomains($transcriptId)
{
global $db_connection;
$domainsQuery = mysqli_query($db_connection, "SELECT * FROM domains LEFT JOIN domains_desc ON domains.pfam_name = domains_desc.pfam_name WHERE
transcript_id LIKE '{$transcriptId}.%' AND evalue < 1e-01 ORDER BY start_point ASC");
$countForDomains = mysqli_num_rows($domainsQuery);
if ($countForDomains == 0)
return null;
return $domainsQuery;
}
function getProteinDomains($convart_ids)
{
global $db_connection;
$domainsQuery = mysqli_query($db_connection, "SELECT * FROM domains_new LEFT JOIN domain_desc_new ON domains_new.pfam_domain_id = domain_desc_new.pfam_domain_id
WHERE domains_new.uniprot_id IN (SELECT db_id FROM convart_gene_to_db WHERE db = 'UNIPROT' AND convart_gene_id IN ({$convart_ids}))");
$countForDomains = mysqli_num_rows($domainsQuery);
if ($countForDomains == 0)
return null;
return $domainsQuery;
}
function getUniprotIdByConvartId($convart_ids)
{
global $db_connection;
$uniprotQuery = mysqli_query($db_connection, "SELECT GROUP_CONCAT(db_id) AS db_id FROM convart_gene_to_db WHERE db = 'UNIPROT' AND convart_gene_id = '{$convart_ids}'");
$uniprotIDs = mysqli_fetch_array($uniprotQuery);
return $uniprotIDs['db_id'];
}
function getClinvarStatsBySignificance($id, $col = 'gene_id')
{
global $db_connection;
global $clinicalSignificanceMapping;
#Statistics
$ClinVarStatisticsQuery = mysqli_query($db_connection, "SELECT clinical_significance, COUNT(clinvar_id) as n_variations " .
"FROM clinvar WHERE `{$col}` IN ({$id}) GROUP BY clinical_significance");
$counts = [];
while ($row = mysqli_fetch_array($ClinVarStatisticsQuery)) {
foreach ($clinicalSignificanceMapping as $key => $listOfSignificances) {
if (in_array($row["clinical_significance"], $listOfSignificances)) {
if (isset($counts[$key])) {
$counts[$key] += $row["n_variations"];
} else {
$counts[$key] = $row["n_variations"];
}
}
}
}
return $counts;
}
function printify($data)
{
$data = normalizeIds($data);
return str_replace('"', '', str_replace(',', ', ', $data));
}
function normalizeIds($transcriptId)
{
if (is_array($transcriptId)) {
$transcriptIds = array_map(function ($x) {
return str_replace('"', '', $x);
}, array_unique($transcriptId));
$transcriptId = '"' . implode('","', $transcriptIds) . '"';
}
return $transcriptId;
}
#gnomAD Chart Stats
function getgnomADStats($transcriptId, $column = 'canonical_transcript')
{
global $db_connection;
$transcriptId = normalizeIds($transcriptId);
$gnomADStatisticsQuery = mysqli_query($db_connection, "SELECT consequence, COUNT(id) FROM gnomad WHERE gnomad.{$column} IN ({$transcriptId}) GROUP BY consequence");
$countsForgnomAD = [];
while ($row = mysqli_fetch_assoc($gnomADStatisticsQuery)) {
$countsForgnomAD[$row['consequence']] = $row['COUNT(id)'];
}
//print_r($countsForgnomAD);
return $countsForgnomAD;
}
#COSMIC Chart Stats
function getCosmicStats($transcriptId, $column = 'accession_number')
{
global $db_connection;
$transcriptId = normalizeIds($transcriptId);
$CosmicStatisticsQuery = mysqli_query($db_connection, "SELECT mutation_description, COUNT(cme_id) FROM CosmicMutantExport WHERE CosmicMutantExport.{$column} IN ({$transcriptId}) GROUP BY mutation_description");
$countsForCosmic = [];
while ($row = mysqli_fetch_assoc($CosmicStatisticsQuery)) {
$countsForCosmic[$row['mutation_description']] = $row['COUNT(cme_id)'];
}
//print_r($countsForCosmic);
return $countsForCosmic;
}
#dbSNP Chart Stats
function getdbSNPStats($transcriptId, $column = 'Feature')
{
global $db_connection;
$transcriptId = normalizeIds($transcriptId);
$dbSNPStatisticsQuery = mysqli_query($db_connection, "SELECT Impact, COUNT(dbsnp_index) FROM dbsnp WHERE dbsnp.{$column} IN ({$transcriptId}) GROUP BY Impact");
$countsFordbSNP = [];
while ($row = mysqli_fetch_assoc($dbSNPStatisticsQuery)) {
$countsFordbSNP[$row['Impact']] = $row['COUNT(dbsnp_index)'];
}
return $countsFordbSNP;
}
#TopMed Chart Stats
function getTopMedStats($transcriptId, $column = 'ensm_transcript_id')
{
global $db_connection;
$transcriptId = normalizeIds($transcriptId);
$TopMedStatisticsQuery = mysqli_query($db_connection, "SELECT COUNT(id) FROM dbsnp_new WHERE dbsnp_new.{$column} IN ({$transcriptId})");
$countsForTopMed = 0;
if (mysqli_num_rows($TopMedStatisticsQuery) == 0) {
$countsForTopMed = 0;
}
else {
$row = mysqli_fetch_assoc($TopMedStatisticsQuery);
$countsForTopMed = $row['COUNT(id)'];
}
#while ($row = mysqli_fetch_assoc($TopMedStatisticsQuery)) {
# $countsForTopMed= $row['COUNT(id)'];
#}
return $countsForTopMed;
}
#PTM Chart Stats
function getPTMStats($transcriptId, $column = 'acc_id')
{
global $db_connection;
$transcriptId = normalizeIds($transcriptId);
$PtmStatisticsQuery = mysqli_query($db_connection, "SELECT ptm_type, COUNT(index_id) FROM ptm WHERE {$column} IN ({$transcriptId}) GROUP BY ptm_type");
$countsForPTM = [];
while ($row = mysqli_fetch_assoc($PtmStatisticsQuery)) {
$countsForPTM[$row['ptm_type']] = $row['COUNT(index_id)'];
}
//print_r($countsForPTM);
return $countsForPTM;
}
function getClinvarData($transcriptId, $column = 'gene_id')
{
global $db_connection;
if ($transcriptId == null)
return null;
$transcriptId = normalizeIds($transcriptId);
$query = mysqli_query($db_connection, "SELECT * FROM clinvar WHERE {$column} IN ({$transcriptId}) ORDER BY position");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getPtmData($transcriptId, $column = 'acc_id', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT {$cols} FROM ptm WHERE {$column} IN ({$transcriptId}) ORDER BY position");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getHMOrthologData($humanId, $mouseId, $wormId)
{
global $db_connection;
if ($humanId == null || $mouseId == null || $wormId == null)
return null;
$query = mysqli_query($db_connection,
"SELECT Human_Variation, Mouse_Significance FROM human_mouse_orthologous as hmo
INNER JOIN convart_gene_to_db as cgd1
INNER JOIN convart_gene_to_db as cgd2
INNER JOIN convart_gene_to_db as cgd3
WHERE cgd1.convart_gene_id = {$humanId}
AND cgd2.convart_gene_id = {$mouseId}
AND cgd3.convart_gene_id = {$wormId}
AND hmo.Human_Protein_ID = cgd1.db_id
AND hmo.Mouse_Protein_ID = cgd2.db_id
AND hmo.C_elegans_Protein_ID = cgd3.db_id;");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getHCOrthologData($humanId, $mouseId, $wormId)
{
global $db_connection;
if ($humanId == null || $mouseId == null || $wormId == null)
return null;
$query = mysqli_query($db_connection,
"SELECT Human_Variation, C_elegans_Significance FROM human_celegans_orthologous as hco
INNER JOIN convart_gene_to_db as cgd1
INNER JOIN convart_gene_to_db as cgd2
INNER JOIN convart_gene_to_db as cgd3
WHERE cgd1.convart_gene_id = {$humanId}
AND cgd2.convart_gene_id = {$mouseId}
AND cgd3.convart_gene_id = {$wormId}
AND hco.Human_Protein_ID = cgd1.db_id
AND hco.Mouse_Protein_ID = cgd2.db_id
AND hco.C_elegans_Protein_ID = cgd3.db_id;");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getHMCOrthologData($humanId, $mouseId, $wormId)
{
/*
global $db_connection;
if ($humanId == null || $mouseId == null || $wormId == null)
return null;
$query = mysqli_query($db_connection,
"SELECT Human_Variation FROM human_celegans_orthologous as hco
INNER JOIN convart_gene_to_db as cgd1
INNER JOIN convart_gene_to_db as cgd2
INNER JOIN convart_gene_to_db as cgd3
WHERE cgd1.convart_gene_id = {$humanId}
AND cgd2.convart_gene_id = {$mouseId}
AND cgd3.convart_gene_id = {$wormId}
AND hco.Human_Protein_ID = cgd1.db_id
AND hco.Mouse_Protein_ID = cgd2.db_id
AND hco.C_elegans_Protein_ID = cgd3.db_id;");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
*/
return 0;
}
function getCommunityData($transcriptId, $column = 'protein_id', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT {$cols} FROM community_variants WHERE {$column} IN ({$transcriptId}) AND validation = 1 ORDER BY protein_pos");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getGO_AnnotationData($geneID, $column = 'gene_id', $cols = '*')
{
global $db_connection;
if ($geneID == null)
return null;
$query = mysqli_query($db_connection, "SELECT {$cols} , GROUP_CONCAT(go_term_evidence_code) AS evidence_codes FROM go_annotation WHERE {$column} IN ({$geneID}) GROUP BY go_term_acc, gene_id ORDER BY go_term_acc");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function validateCommunityVariant($validation_code)
{
global $db_connection;
$query = mysqli_query($db_connection, "UPDATE community_variants SET `validation` = 1 WHERE validation_code = '$validation_code';");
if (mysqli_affected_rows($db_connection) == 0) {
echo '<script>alert("Update Failed, Try Again!")</script>';
return "Please try again later!";
}
$row = mysqli_fetch_assoc($query);
header('Location: https://convart.org');
return true;
}
function getMouseVariantsData($transcriptId)
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT * FROM mouse_variants_new WHERE refseq_id = '$transcriptId' ORDER BY pos");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getCosmicData($transcriptId, $column = 'accession_number', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT $cols FROM CosmicMutantExport WHERE {$column} IN ({$transcriptId}) ORDER BY position DESC");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getdbSNPData($transcriptId, $column = 'Feature', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT $cols FROM dbsnp WHERE {$column} IN ({$transcriptId}) ORDER BY Protein_position DESC");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getTopMedData($transcriptId, $column = 'ensm_transcript_id', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT $cols FROM dbsnp_new WHERE {$column} IN ({$transcriptId}) ORDER BY position DESC");
if (mysqli_num_rows($query) == 0)
return null;
return $query;
}
function getCelVariantsData($transcriptId, $column = 'refseq_id', $cols = '*')
{
global $db_connection;
if ($transcriptId == null)
return null;
$query = mysqli_query($db_connection, "SELECT $cols FROM celegans_variants WHERE refseq_id = '$transcriptId'");
if (mysqli_num_rows($query) == 0){
return null;
}
return $query;
}
function searchProteinNumbers($value)
{
global $db_connection;
$value = str_replace('"', '', $value);
if (empty($value))
return [];
$ids = [];
$ids[] = "SUBSTRING_INDEX(nc_prot.meta_value, '.', 1)";
$ids = implode(',', $ids);
$query = mysqli_query($db_connection, "SELECT GROUP_CONCAT(DISTINCT CONCAT(cdb.convart_gene_id, ',', cdb.db_id, ',', nc_sym.meta_value, ',', nc_spec.meta_value) SEPARATOR ';')
AS data, nc_prot.ncbi_gene_id FROM ncbi_gene_meta AS nc_search INNER JOIN ncbi_gene_meta AS nc_spec ON
nc_search.ncbi_gene_id=nc_spec.ncbi_gene_id AND nc_spec.meta_key='species_id' INNER JOIN ncbi_gene_meta AS nc_sym ON
nc_search.ncbi_gene_id=nc_sym.ncbi_gene_id AND nc_sym.meta_key='gene_symbol' INNER JOIN ncbi_gene_meta AS nc_prot ON
nc_search.ncbi_gene_id=nc_prot.ncbi_gene_id AND nc_prot.meta_key='protein_number' INNER JOIN convart_gene_to_db AS cdb ON
cdb.db_id=nc_prot.meta_value
#INNER JOIN msa_gene AS mg ON
#mg.convart_gene_id=cdb.convart_gene_id
#INNER JOIN msa_best_combination AS mb ON
#mb.msa_id = mg.msa_id
WHERE nc_search.meta_value IN ('{$value}') OR nc_search.ncbi_gene_id IN ('{$value}')
GROUP BY nc_prot.ncbi_gene_id");
# MSA'sı olmayanlar orth-searchde cikmiyordu
$searchResultBySpecies = [];
while ($row = mysqli_fetch_assoc($query)) {
$transcriptIds = explode(';', $row['data']);
foreach ($transcriptIds as $data) {
$data = explode(',', $data);
$species = $data[3];
if (!isset($searchResultBySpecies[$species])) {
$searchResultBySpecies[$species] = [];
}
$searchResultBySpecies[$species][] = [
'convart_gene_id' => $data[0],
'transcript_id' => $data[1], 'gene_symbol' => $data[2],
'ncbi_gene_id' => $row['ncbi_gene_id']
];
}
}
return $searchResultBySpecies;
}
function getHumanVariationCount($prot_ids)
{
global $db_connection;
$variation_count = 0;
$prot_id_list = explode(",", $prot_ids);
foreach ($prot_id_list as &$prot){
if (substr($prot, 0, 2) == 'NP'){
$clinvarCounts = getClinvarStatsBySignificance('"'.$prot.'"', 'np_id');
$variation_count += array_sum($clinvarCounts);
}
elseif (substr($prot, 0, 4) == 'ENST'){
$variation_count += array_sum(getgnomADStats('"'.$prot.'"'));
$variation_count += array_sum(getdbSNPStats(@'"'.$prot.'"'));
$variation_count += array_sum(getCosmicStats(@'"'.$prot.'"'));
$variation_count += getTopMedStats(@'"'.$prot.'"');
}
else {
$variation_count += array_sum(getPTMStats('"'.$prot.'"'));
}
}
return $variation_count;
}
function getMouseVariationCount($prot_ids)
{
global $db_connection;
$variation_count = 0;
$prot_id_list = explode(",", $prot_ids);
foreach ($prot_id_list as &$prot){
$query = getMouseVariantsData($prot);
$variation_count += mysqli_num_rows($query);
}
return $variation_count;
}
function getWormVariationCount($prot_ids)
{
global $db_connection;
$variation_count = 0;
$prot_id_list = explode(",", $prot_ids);
foreach ($prot_id_list as &$prot){
$query = getCelVariantsData($prot);
$variation_count += mysqli_num_rows($query);
#$variation_count += 1;
#die($query);
}
return $variation_count;
}
function search_spemud_proteins($spemud_value)
{
global $db_connection;
if (empty($spemud_value))
return null;
$queryIds = mysqli_query($db_connection, "SELECT DISTINCT nc2.ncbi_gene_id AS human_gene_id, homology.mouse_gene_id, homology.worm_gene_id
FROM ncbi_gene_meta AS nc1
INNER JOIN ncbi_gene_meta AS nc2 ON nc1.ncbi_gene_id=nc2.ncbi_gene_id
INNER JOIN homology ON nc2.ncbi_gene_id = homology.human_gene_id
WHERE nc1.meta_value='homo sapiens'
AND nc2.meta_value='$spemud_value'");
if (mysqli_num_rows($queryIds) == 0) {
return null;
}
$spemudGeneIdList = [
"human" => "",
"mouse" => "",
"worm" => "",
];
$blockResults = "";
$humanResults = "<div id='human' class='row pageTitle'>Results for Homo Sapiens <hr></div>";
$mouseResults = "<div id='mouse' class='row pageTitle'>Results for Mus Musculus <hr></div>";
$wormResults = "<div id='worm' class='row pageTitle'>Results for Caenorhabditis Elegans <hr></div>";
$colors = ['#d50000', '#1a237e', '#006064', '#f57f17', '#3e2723'];
$colId = 0;
while ($row = mysqli_fetch_assoc($queryIds)) {
$spemudGeneIdList["human"] = $row["human_gene_id"];
$spemudGeneIdList["mouse"] = $row["mouse_gene_id"];
$spemudGeneIdList["worm"] = $row["worm_gene_id"];
foreach ($spemudGeneIdList as $key => $value) {
$geneIdList = explode(",", $value);
$species = ucwords($key);
$totalResultCount = 0;
$html_outputs = array ();
for ($i = 0; $i < count($geneIdList); $i++) {
$tempGeneIds = $geneIdList[$i];
$queryProteinIds = mysqli_query($db_connection, "SELECT nc1.ncbi_gene_id, nc2.meta_value AS gene_symbol,
GROUP_CONCAT(DISTINCT nc1.meta_value) AS prot_ids, cdb.convart_gene_id
FROM ncbi_gene_meta AS nc1
INNER JOIN ncbi_gene_meta AS nc2 ON nc1.ncbi_gene_id=nc2.ncbi_gene_id
INNER JOIN convart_gene_to_db AS cdb ON nc1.meta_value=cdb.db_id
WHERE nc1.ncbi_gene_id='$tempGeneIds'
AND nc1.meta_key='protein_number'
AND nc2.meta_key='gene_symbol'
GROUP BY cdb.convart_gene_id");
$totalResultCount += mysqli_num_rows($queryProteinIds);
// Get transcripts for each gene in each organism
while ($row_prots = mysqli_fetch_assoc($queryProteinIds)) {
$temp_gene_symbol = $row_prots['gene_symbol'];
$temp_prot_ids = $row_prots['prot_ids'];
$temp_convart_ids = $row_prots['convart_gene_id'];
$queryCheckMSA = mysqli_query($db_connection, "SELECT * FROM `msa_gene` WHERE convart_gene_id = '$temp_convart_ids'");
if (mysqli_num_rows($queryCheckMSA) == 0) {
continue;
}
$prot_id_enst_control = explode(",", $temp_prot_ids);
#if (count($prot_id_enst_control) == 1 && substr($prot_id_enst_control[0], 0, 7) == 'ENSMUST'){
# continue;
#}
$variation_count = "";
if (strcmp($key, "human") == 0){
$variation_count = getHumanVariationCount($temp_prot_ids);
}
elseif (strcmp($key, "mouse") == 0){
$variation_count = getMouseVariationCount($temp_prot_ids);
}
elseif (strcmp($key, "worm") == 0){
$variation_count = getWormVariationCount($temp_prot_ids);
}
$spemud_radio_button = "<div class='convart-radio'><input id='$key-$temp_convart_ids' name='$key' value='$temp_convart_ids' type='radio' /> <label style='color:$colors[$colId];' for='$key-$temp_convart_ids'>GeneID: $tempGeneIds | $temp_gene_symbol | $temp_prot_ids | $variation_count</label></div>";
$row_input = array($spemud_radio_button, $variation_count);
array_push($html_outputs, $row_input);
}
}
$ranks = array_column($html_outputs, 1);
array_multisort($ranks, SORT_DESC, $html_outputs);
for ($j = 0; $j < count($html_outputs); $j++) {
if (strcmp($key, "human") == 0) {
$humanResults .= $html_outputs[$j][0];
} else if (strcmp($key, "mouse") == 0) {
$mouseResults .= $html_outputs[$j][0];
} else if (strcmp($key, "worm") == 0) {
$wormResults .= $html_outputs[$j][0];
}
}
}
$colId += 1 % 5;
}
if (strcmp($humanResults, "<div class='row pageTitle'>Results for Homo Sapiens <hr></div>") == 0) {
$humanResults .= 'No homolog transcript found for this species.';
}
if (strcmp($mouseResults, "<div class='row pageTitle'>Results for Mus Musculus <hr></div>") == 0) {
$mouseResults .= 'No homolog transcript found for this species.';
}
if (strcmp($wormResults, "<div class='row pageTitle'>Results for Caenorhabditis Elegans <hr></div>") == 0) {
$wormResults .= 'No homolog transcript found for this species.';
}
$blockResults .= $humanResults;
$blockResults .= $mouseResults;
$blockResults .= $wormResults;
return $blockResults;
}
function getGeneIdbyDBId($id, $db = 'NM')
{
global $db_connection;
$idWithoutVersion = explode('.', $id)[0];
$versionOfId = explode('.', $id)[1];
$query = mysqli_query($db_connection, "SELECT convart_gene_id FROM convart_gene_to_db WHERE db='{$db}' AND db_id='$idWithoutVersion'");
if ($query == null || mysqli_num_rows($query) == 0) {
return null;
}
return mysqli_fetch_assoc($query)['convart_gene_id'];
}
function getGeneByRSNumber($rs_number)