$intervalEnd[$i] = bp2cM($regionChr[$i], (int) $regionEnd[$i], $experiment1['species']); } $chromosomsEx1 = $regionChr; $ex1 = get_loci_from_sql($database1, $experiment1['connection'], 'userinterval', $chromosomsEx1, $confidence_int, $group2region, $intervalStart, $intervalEnd); if (!empty($ex1)) { // converts $ex1 in 2 arrays: $groups1 = groupnr -> ('loci' -> lociOfGroup, 'start', 'end', 'Chr') $mapEx1 = index -> (locus,groupNr) list($groups1, $mapEx1) = $ex1; } else { echo '<INPUT TYPE=BUTTON VALUE="back" onClick="history.back()">'; echo '<br />'; fatal_error('nothing found for the given region(-s)'); } // generates an arrays with index -> locinames // $loci_ex1 = array_map('current',$mapEx1); $chromosomsEx2 = getChromosomes($compara, $experiment2['ensembl_species']); //filter compara chromosoms for existing chromosoms in QTL-database $chromosomsEx2 = filter_chromos($experiment2['connection'], array_flip($chromosomsEx2)); $chromosomsEx2 = array_flip($chromosomsEx2); $ex2 = get_loci_from_sql($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'])); $dbs = array($database1, $database2); $groupSynteny_ex12ex2 = getSyntenyGroups(array($experiment1['connection'], $experiment2['connection']), $compara, $groups1, $groups2, $species_names, $genome_db_ids, $dbs); // display ----------------------- include 'display_table.php'; toc($start, 'Synteny search'); require_once "../eqtl/footer.php";
<?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])) { $confidence_int_len = $args[$confidence_int_str]; } else {
$chrs = filter_chromos($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, $dbs); // h**o useDB($database1, $experiment1['connection']); $loci2stable_ids_ex1 = loci2stable_ids($loci_ex1, $experiment1['connection']);