GENOME: whole-genome record

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Starting code

This is the PHP code used by this example.

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public function parseGenomeRecord()
{
    $parser = DatabaseParserFactory::createParser("GENOME");
    $parser->parseDataFile(file($this->getParameter('kernel.project_dir') . '/public/data/sample.genome'));
 
    return $this->render('default/parseGenomeRecord.html.twig',
        [
            'organism'      => $parser->getOrganism(),
            'commonName'    => $parser->getCommonName(),
            'taxClass'      => $parser->getTaxClass(),
            'isComplete'    => $parser->getIsComplete(),
            'gbRelease'     => $parser->getGbRelease(),
            'gbEntries'     => $parser->getGbEntries(),
            'gbBasepairs'   => $parser->getGbBasepairs(),
            'size'          => $parser->getSize(),
        ]
    );
}
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Result

Result returned by BioPHP for the demonstration data.

Parsed record
OrganismHomo sapiens
Common namehuman
Taxonomic class
  • 0 : Eukaryota
  • 1 : Metazoa
  • 2 : Chordata
  • 3 : Craniata
  • 4 : Vertebrata
  • 5 : Mammalia
Is completeNO
GenBank release134
GenBank entries1234567
GenBank basepairs9876543210
Genome size (bp)3200000000

The code above is the one actually executed by this page. Find the other examples in the left-hand column, or the tools in BioTools.