where Chr = ' . $chr1 . '
and cMorgan >= ' . $start1 . '
and cMorgan <= ' . $end1 . ';';
$loci_ex1 = get_only_loci_from_sql($sql, $experiment1['connection']);
$db2 = $experiment2["db_name"];
$sql = 'select Name from ' . $db2 . '.locus
where Chr = ' . $chr2 . '
and cMorgan >= ' . $start2 . '
and cMorgan <= ' . $end2 . ';';
$loci_ex2 = get_only_loci_from_sql($sql, $experiment2['connection']);
// Loci to genes
useDB($db1, $experiment1['connection']);
$loci2stable_ids_ex1 = loci2stable_ids($loci_ex1, $experiment1['connection']);
$unique_ens_ids_ex1 = get_unique_vals_from_2d_array($loci2stable_ids_ex1[0]);
useDB($db2, $experiment2['connection']);
$loci2stable_ids_ex2 = loci2stable_ids($loci_ex2, $experiment2['connection']);
$unique_ens_ids_ex2 = get_unique_vals_from_2d_array($loci2stable_ids_ex2[0]);
//exit('Exit: Debbuging in compara.php!');
// HOMOLOGY => do it on the fewer genes
$n_ens_ids_ex1 = sizeof($unique_ens_ids_ex1);
$n_ens_ids_ex2 = sizeof($unique_ens_ids_ex2);
$traits12traits2 = array();
if ($n_ens_ids_ex1 < $n_ens_ids_ex2) {
// homology on experiment 1
$homology_ex1 = get_homologue_ens_ids($compara, $unique_ens_ids_ex1, $experiment2['ensembl_species']);
//intersection
foreach ($homology_ex1 as $unique_id_ex1 => $corr_homologue_ens_ids_ex2) {
$intersect = array_intersect(array_keys($corr_homologue_ens_ids_ex2), $unique_ens_ids_ex2);
foreach ($intersect as $id_ex2) {
$traits12traits2[$unique_id_ex1][$id_ex2] = $corr_homologue_ens_ids_ex2[$id_ex2];
}
// display arguments:
//include 'display_args.php';
// SYNTENY
$species_names = array("Mus musculus", "Rattus norvegicus");
$genome_db_ids = array(57, 3);
$dbs = array('eqtl_rostock_eae', 'eqtl_stockholm_eae_logplier');
$synteny_ex12ex2 = getSynteny($qtldb, $compara, $loci_ex1, $loci_ex2, $species_names, $genome_db_ids, $dbs);
// Loci to genes
//"Mus musculus"
useDB('eqtl_rostock_eae', $qtldb);
//loci2stable_
$loci2stable_ids_ex1 = loci2stable_ids($loci_ex1, $qtldb);
$unique_ens_ids_ex1 = get_unique_vals_from_2d_array($loci2stable_ids_ex1[0]);
//"Rat"
useDB('eqtl_stockholm_eae_logplier', $qtldb);
$loci2stable_ids_ex2 = loci2stable_ids($loci_ex2, $qtldb);
$unique_ens_ids_ex2 = get_unique_vals_from_2d_array($loci2stable_ids_ex2[0]);
// HOMOLOGY => do it on the fewer
$n_loci_ex1 = sizeof($unique_ens_ids_ex1);
$n_loci_ex2 = sizeof($unique_ens_ids_ex2);
$traits12traits2 = array();
if ($n_loci_ex1 < $n_loci_ex2) {
$homology_ex1 = get_homologue_ens_ids($compara, $unique_ens_ids_ex1, $genome_db_ids[1]);
//intersection
foreach ($homology_ex1 as $unique_id_ex1 => $corr_homologue_ens_ids_ex1) {
$traits12traits2[$unique_id_ex1] = array_intersect($corr_homologue_ens_ids_ex1, $unique_ens_ids_ex2);
}
} else {
$homology_ex2 = get_homologue_ens_ids($compara, $unique_ens_ids_ex2, $genome_db_ids[0]);
//intersection
foreach ($unique_ens_ids_ex1 as $id_ex1) {
<?php
include 'html/header.html';
require_once 'db_functions.php';
require_once 'qtl_functions.php';
require_once 'utils.php';
require_once 'fill_related_projects.php';
fill_compara_array();
connectToQtlDBs(array('Ratte'));
global $compara_array;
$db = $compara_array['Ratte']['connection'];
useDB('eqtl_stockholm_eae_logplier', $db);
//useDB('eqtl_rostock_eae', $db);
$loci = array('c1.loc1', 'c1.loc10', 'c1.loc100', 'c1.loc101', 'c1.loc102', 'c1.loc103', 'c1.loc104', 'c1.loc105', 'c1.loc106', 'c1.loc107', 'c1.loc108', 'c1.loc109', 'c1.loc11', 'c1.loc110', 'c1.loc111', 'c1.loc112', 'c1.loc113', 'c1.loc114', 'c1.loc115');
//$loci = array('c9.loc48', 'c9.loc43', 'c9.loc40' , 'c9.loc39');
loci2stable_ids_new($loci, $db);
loci2stable_ids_new($loci, $db);
$t = tic();
print_r(loci2stable_ids_new($loci, $db));
print "<br>";
print "<br>";
toc($t, 'opt');
print "<br>";
print "<br>";
$t = tic();
print_r(loci2stable_ids($loci, $db));
print "<br>";
print "<br>";
toc($t, 'normal');
include 'html/footer.html';
