Exemplo n.º 1
0
    $end2 = substr($region2, $pos + 1);
    //  fetch loci
    $genome_id1 = $species2genome_db_ids[$species1];
    $db1 = $genome_ids2dbs[$genome_id1];
    $sql = 'select Name from ' . $db1 . '.Locus
where Chr = ' . $chr1 . ' 
and cMorgan >= ' . $start1 . ' 
and cMorgan <= ' . $end1 . ';';
    $loci_ex1 = get_only_loci_from_sql($sql, $qtldb);
    $genome_id2 = $species2genome_db_ids[$species2];
    $db2 = $genome_ids2dbs[$genome_id2];
    $sql = 'select Name from ' . $db2 . '.Locus
where Chr = ' . $chr2 . ' 
and cMorgan >= ' . $start2 . ' 
and cMorgan <= ' . $end2 . ';';
    $loci_ex2 = get_only_loci_from_sql($sql, $qtldb);
    //
    //	// mus whole chromosom
    //	$ex1 =  get_loci_from_sql('eqtl_rostock_eae', $qtldb, 'userinterval', $chromosomNo, $confidenceInterval, 80, 110);
    //	// converts $ex1 in 2 arrays: $groups1 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end') $maxEx1 = index -> (locus,groupNr)
    //	list($groups1, $mapEx1) = $ex1;
    //	// generates an arrays with index -> locinames
    //	$loci_ex1 = array_map('current',$mapEx1);
    //	// generates an assoc. arrays with locinames -> groupnr
    //	foreach ($mapEx1 as $arrayValue) {
    //		$groupLoci1[$arrayValue[0]]= $arrayValue[1];
    //	}
    //	// rat whole chromosom
    //	$ex2 =  get_loci_from_sql('eqtl_stockholm_eae_logplier', $qtldb, 'userinterval', $chromosomNo, $confidenceInterval, 137	,138);
    //	// converts $ex2 in 2 arrays: $groups2 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end') $maxEx2 = index -> (locus,groupNr)
    //	list($groups2, $mapEx2) = $ex2;
Exemplo n.º 2
0
$start1 = $end1 = $chr1 = $start2 = $end2 = $chr2 = 0;
getReg($region1, $chr1, $start1, $end1);
getReg($region2, $chr2, $start2, $end2);
//  fetch loci
$db1 = $experiment1["db_name"];
$sql = 'select Name from ' . $db1 . '.locus
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']);