</div>
<br style="clear: both;" />
<?php
if ($projects[0] == NULL || $projects[0] == "NULL") {
include "../eqtl/footer.php";
exit;
}
// only the database of the source project needs to be opened
$src_proj = $projects[0];
connectToQtlDBs(array($src_proj));
$qtldb = $compara_array[$src_proj]['connection'];
$compara = connectToCompara();
// region selection
// fetch chromosomes to species id
$ens_species = $compara_array[$src_proj]['ensembl_species'];
$chrs = getChromosomesAndLengths($compara, $ens_species);
// additional filtering
$chrs = filter_chromos($qtldb, $chrs);
$species = $compara_array[$src_proj]['species'];
// get selected regions
$chr2reg = array();
if (isset($args[$reg_str])) {
$regs = $args[$reg_str];
foreach ($regs as $reg) {
$pos = strpos($reg, ":");
$chr2reg[substr($reg, 0, $pos)][] = substr($reg, $pos + 1);
}
}
//confidence intervall
$confidence_int_str = 'confidence_int';
if (isset($args[$confidence_int_str])) {
$chrs = getChromosomesAndLengths($compara, $experiment1['ensembl_species']);
// additional filtering
useDB($database1, $experiment1['connection']);
$chrs = filter_chromos($experiment1['connection'], $chrs);
$chromosomsEx1 = array_keys($chrs);
//getChromosoms($compara, $experiment1['genome_db_id']);
//initialize array for mapping groupnumbers to regions
$group2region = array();
$ex1 = get_loci_from_sql($database1, $experiment1['connection'], 'wholeGenome', $chromosomsEx1, $confidence_int, $group2region);
// converts $ex1 in 2 arrays: $groups1 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end', 'Chr') $mapEx1 = index -> (locus,groupNr)
list($groups1, $mapEx1) = $ex1;
// generates an arrays with index -> locinames
$loci_ex1 = array_map('current', $mapEx1);
$groupnr_ex1 = array_map('next', $mapEx1);
$loci2group1 = array_combine($loci_ex1, $groupnr_ex1);
$chrs = getChromosomesAndLengths($compara, $experiment2['ensembl_species']);
// additional filtering
useDB($database2, $experiment2['connection']);
$chrs = filter_chromos($experiment1['connection'], $chrs);
$chromosomsEx2 = array_keys($chrs);
//getChromosoms($compara, $experiment1['genome_db_id']);
//initialize array for mapping groupnumbers to regions
$group2region2 = array();
$ex2 = get_loci_from_sql($database2, $experiment2['connection'], 'wholeGenome', $chromosomsEx2, $confidence_int, $group2region2);
// converts $ex2 in 2 arrays: $groups2 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end') $mapEx2 = index -> (locus,groupNr)
list($groups2, $mapEx2) = $ex2;
// generates an arrays with index -> locinames
$loci_ex2 = array_map('current', $mapEx2);
// SYNTENY
$genome_db_ids = getGenomeDBIDs($compara, array($experiment1['ensembl_species'], $experiment2['ensembl_species']));
$groupSynteny_ex12ex2 = getSyntenyGroups(array($experiment1['connection'], $experiment2['connection']), $compara, $groups1, $groups2, $species_names, $genome_db_ids, $dbs);
