function groups2bps($qtl_db, $groups, $species)
{
$bp = array();
$i = 0;
foreach ($groups as $group) {
$bp[$i]['start'] = cM2bp($group['Chr'], $group['start'], $species);
$bp[$i]['end'] = cM2bp($group['Chr'], $group['end'], $species);
$i++;
}
return $bp;
}
echo "<!-- QTL known to overlap with gene location -->\n";
echo "</td>\n";
*/
echo "<td nowrap>";
}
if ($prevTrait == $row1["trait_id"]) {
echo "<br />";
}
$col = "black";
if ($row1["qtl_Chromosome"] == $row1["chromosome"]) {
$col = "red";
}
echo "<font color='{$col}'>";
echo $row1["qtl_Chromosome"] . ":" . $row1["qtl_cMorgan_Peak"] . " " . (empty($row1["qtl_covariates"]) ? "none" : $row1["qtl_covariates"]) . ":" . $row1["qtl_lod"];
if (!empty($row1["qtl_Chromosome"]) and isset($row1["qtl_cMorgan_Peak"]) and "" != $row1["qtl_cMorgan_Peak"]) {
$bp = cM2bp($row1["qtl_Chromosome"], $row1["qtl_cMorgan_Peak"]);
//echo("!!!bp=$bp!!!");
$overlapping_qtl = withinthefollowingqtls($row1["qtl_Chromosome"], $bp, $public_qtls, FALSE);
if (!empty($overlapping_qtl) and 0 < count($overlapping_qtl)) {
echo " (<font color='green'><b>";
echo join(",", $overlapping_qtl);
echo "</b></font>)";
}
//print_r($overlapping_qtl);
}
echo "</font>";
$prevTrait = $row1["trait_id"];
}
if (!empty($prevTrait)) {
echo "</td></tr>\n";
}
$tmp_species = array_combine($names, array_fill(0, 3, ""));
fwrite($fptr, "Locus\tstart\tstop\t" . implode("\t", $names) . "\r\n");
# synreg
#Locus group chr start stop Trait Status Syngroup chr start end Trait homotype syn_ids
$size = count($genelist);
for ($i = 1; $i < $size; $i++) {
// skip header
$entry = explode("\t", $genelist[$i]);
$syn_list = explode(",", $entry[13]);
foreach ($names as $name) {
$tmp_species[$name] = "";
}
//array_fill_keys($names, "");
//get all intersecting disease species
for ($j = 0; $j < $size_d - 1; $j++) {
// skip header
$intersect = array_intersect($syn_list, $synIDs_d[$j]);
if (!empty($intersect)) {
// synteny => add species to list
$tmp_species[$species_d[$j]] = "x";
}
}
$chr = $entry[2];
$start = cM2bp($chr, $entry[3], $species1);
$end = cM2bp($chr, $entry[4], $species1);
$str = $entry[0] . "\t" . $start . "\t" . $end . "\t" . implode("\t", $tmp_species);
fwrite($fptr, $str . "\r\n");
}
fclose($fptr);
echo "done synteny to disease regions";
include 'html/footer.html';