/**
* @Route("/")
* @Route("/hello/{name}")
* @Template()
*/
public function indexAction($name = "guest")
{
$fasta_in = new FastAFile(new \SplFileObject("/tmp/dmel-all-chromosome-r5.47.fasta"));
$fasta_out = new FastAFile(new \SplFileObject("/tmp/test-output.fasta"));
foreach ($fasta_out->getSequences() as $sequence) {
$fasta_out->removeSequence($sequence);
}
foreach ($fasta_in->getSequences() as $sequence) {
$fasta_out->addSequence($sequence);
}
$fasta_out->save();
return array();
}
/**
* {@inheritDoc}
*/
public function readFile()
{
$file = $this->getWorkingFile();
if ($file == null) {
$this->fileValid = false;
return false;
}
$sequencesRead = 0;
while (!$file->eof()) {
$line = trim($file->current());
if (strlen($line) > 0) {
if (substr($line, 0, 7) == "##FASTA") {
$file->next();
parent::readFile();
} elseif ($line[0] != "#") {
$feature = $this->parseFeature($line);
if ($feature instanceof GFFFeature) {
$this->features[] = $feature;
} elseif ($feature !== null) {
$this->fileValid = false;
return false;
}
}
}
$file->next();
}
$this->fileRead = true;
return $sequencesRead;
}