$end2 = substr($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;
$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']);