The Genes component is a reusable component for Nooku Framework. This is an example!
By installing this component you can easily re-use the functionality its classes offer in your own components.
You can install this extension using Composer. Add the following requirements to your composer.json file in your Joomla application's root directory:
{
"require": {
"stevenrombauts/genes-component": "dev-master"
},
"minimum-stability": "dev"
}Run composer install to take care of downloading and installing the package.
Having your entities extend the ComGenesModelEntityGene class will automatically add support for translating the DNA sequence into a protein sequence. Or call it directly:
$sequence = <<<EOL
> A sequence
ATGCAGACTGACGATTCTTGGAAACATAATGTGTCGTTTTATACA
AATTTGGACTACACCGATAAGGATACCAAAATCAGTGCAGTTTAA
EOL;
$data = array(
'identifier' => 'C02H7.2',
'title' => 'npr-19',
'sequence' => $sequence
);
$entity = KOBjectManager::getInstance()->getObject('com://stevenrombauts/genes.model.entity.gene', array('data' => $data));
echo $entity->protein;You can use the FASTA filter to validate and sanitize strings representings nucleotide sequences or peptide sequences.
Example:
$filter = KObjectManager::getInstance()->getObject('com://stevenrombauts/genes.filter.fasta');
$sequence = <<<EOL
> LCBO - Prolactin precursor - Bovine
; a sample sequence in FASTA format
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPN
EMFNEFDQVIPGAKETEPYPVWSGLPSLQTKDED
ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
EOL;
// This one should be valid:
echo ($filter->validate($sequence) === true ? "Valid sequence" : "Invalid sequence");
// Sanitizing will remove all characters that don't belong (line-breaks, comments, etc ..):
echo $filter->sanitize($sequence);