return $x / $sum * 100;
}, $values, array_fill(0, count($values), array_sum($values)));
fwrite($outputs[$key], $id . "\t" . implode("\t", $norma) . "\n");
}
fclose($outputs[$key]);
}
/*
* Process bowtie mapping stats and write its to common file as table.
*/
$result = $workDir . DIRECTORY_SEPARATOR . $prefix . '.stats.txt';
$output = fopen($result, 'wb');
if ($output) {
fwrite($output, "name\tmapped-to-human\tmapped-to-reference\tn-filtered-reads\tn-reads-total\tfiltered-reads-percent\n");
$outputStrings = array();
foreach ($dirIterator as $dir) {
if (!$dir->isDir() || $dir->isDot() || FileIterator::isHidden($dir->getFilename())) {
continue;
}
$humanBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::HUMAN_FILE);
if (!$humanBowtieStats || !($humanMappingPercent = $humanBowtieStats->getAlignedReadsPercent())) {
$humanMappingPercent = 'NA';
}
$referenceBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::REFERENCE_FILE);
if (!$referenceBowtieStats || !($refernceMappingPercent = $referenceBowtieStats->getAlignedReadsPercent())) {
$relativeToUnmappedMappingPercent = 'NA';
} else {
$relativeToUnmappedMappingPercent = round((100 - $humanMappingPercent) * $refernceMappingPercent / 100, 2);
}
// search for reads filtering stats
$nReadsTotal = 'NA';
$nReadsFiltered = $humanBowtieStats ? $humanBowtieStats->getProcessedReadsCount() : 'NA';
