README

Symfony forms and business logic for the BioPHP minitools.

This package ships the reusable half of the minitools: a Symfony form type and a service (manager) for each tool. It deliberately contains no controller and no template — the consuming application wires the forms into its own controllers and renders them with its own views.

All biological reference data (nucleotides, amino acids, codon tables, restriction endonucleases, vendors…) comes from amelaye/biophp, so nothing is duplicated here.

Requirements

PHP 8.2+
Symfony 7.4
amelaye/biophp, which itself needs JMSSerializerBundle and DoctrineBundle registered in the host application, and network access to api.amelayes-biophp.net (the API adapters fetch reference data over HTTP)

Installation

composer require amelaye/biotools

return [
    // ...
    JMS\SerializerBundle\JMSSerializerBundle::class => ['all' => true],
    Amelaye\BioPHP\AmelayeBioPHPBundle::class => ['all' => true],
    Amelaye\BioTools\AmelayeBioToolsBundle::class => ['all' => true],
];

Usage

Every form type and every manager is available for autowiring. A controller only has to build the form and delegate to the manager:

use Amelaye\BioTools\Form\FindPalindromesType;
use Amelaye\BioTools\Service\FindPalindromeManager;
use Symfony\Bundle\FrameworkBundle\Controller\AbstractController;
use Symfony\Component\HttpFoundation\Request;
use Symfony\Component\HttpFoundation\Response;
use Symfony\Component\Routing\Annotation\Route;

class MinitoolsController extends AbstractController
{
    #[Route('/minitools/find-palindromes', name: 'find_palindromes')]
    public function findPalindromes(Request $request, FindPalindromeManager $manager): Response
    {
        $palindromes = [];
        $form = $this->createForm(FindPalindromesType::class);

        if ($request->isMethod('POST') && $form->handleRequest($request)->isValid()) {
            $data = $form->getData();
            $palindromes = $manager->findPalindromicSeqs($data['seq'], $data['min'], $data['max']);
        }

        return $this->render('find_palindromes.html.twig', [
            'form' => $form->createView(),
            'palindromes' => $palindromes,
        ]);
    }
}

Available tools

Tool	Form type	Manager
Chaos Game Representation of DNA	`ChaosGameRepresentationType`	`ChaosGameRepresentationManager`
Oligonucleotide frequency based distance	`DistanceAmongSequencesType`	`DistanceAmongSequencesManager`
DNA to protein translation	`DnaToProteinType`	`DnaToProteinManager`
Palindromic sequences finder	`FindPalindromesType`	`FindPalindromeManager`
GC content finder	`FastaUploaderType`	`FastaUploaderManager`
Melting temperature (Tm)	`MeltingTemperatureType`	`MeltingTemperatureManager`
Microarray data analysis	`MicroArrayDataAnalysisType`	`MicroarrayAnalysisAdaptiveManager`
Microsatellite repeats finder	`MicrosatelliteRepeatsFinderType`	`MicrosatelliteRepeatsFinderManager`
Nucleotide / oligonucleotide frequency	`OligoNucleotideFrequencyType`	(biophp `OligosManager`)
PCR amplification	`PcrAmplificationType`	`PcrAmplificationManager`
Protein sequence properties	`ProteinPropertiesType`	`ProteinPropertiesManager`
Protein to DNA reverse translation	`ProteinToDnaType`	`ProteinToDnaManager`
Random sequences	`RandomSequencesType`	`RandomSequencesManager`
Reduced alphabets for proteins	`ReduceAlphabetType`	`ReduceProteinAlphabetManager`
Restriction enzyme digest of DNA	`RestrictionEnzymeDigestType`	`RestrictionDigestManager`
Alignment of two sequences	`SequenceAlignmentType`	`SequenceAlignmentManager`
DNA sequence manipulation / properties	`SequenceManipulationType`	`SequenceManipulationAndDataManager`
GC-, AT-, KETO- and oligo-skews	`SkewsType`	`SkewsManager`
Formula functions	`FormulasType`	`FormulasManager`

The upstream Reader (fasta/gff) minitool is not covered: it is a parsing library rather than a form-driven tool, so it belongs with the other parsers in amelaye/biophp. Its original source is kept in legacy/.

Generated graphics

Four tools produce a drawing: Chaos Game Representation (CGR and FCGR), skews and the distance dendrogram. They are rendered as SVG — vector, so crisp at any zoom, with real fonts and styleable with CSS — and written into the directory configured under nucleotids_graphs.path_graphs. Each method returns the path it wrote; the file name carries a random suffix so two concurrent requests cannot overwrite each other's graphic:

$sFile = $chaosGameRepresentationManager->createCGRImage($sName, $sSequence, 300);
// /var/www/created_files/CGR_9f3a1c0e.svg

$aResult = $chaosGameRepresentationManager->createFCGRImage(...);
// ['map' => [...image map coordinates...], 'file' => '.../FCGR_1b7d4a22.svg']

The directory must exist and be writable, otherwise an exception is thrown — the previous GD implementation failed silently and returned a name for a file it had not written.

Configuration

The bundle works without configuration. Two data sets can be overridden:

# config/packages/amelaye_biotools.yaml
amelaye_biotools:
    nucleotids_graphs:
        path_graphs: 'created_files/'   # where generated PNG images are written
        # ... geometry and file names for CGR/FCGR and skew images
    protein_colors:
        # colour palettes for reduced protein alphabets (20, Murphy15, Li10, …)

Defaults live in Resources/config/defaults.php.

Divergences from the original minitools

Two formulas are mathematically wrong in the upstream biophp.org code and have been corrected here (each divergence is commented in Service/FormulasManager.php):

Centigrade to Fahrenheit — the original applies 32 + (C x 0.555); 0.555 (~5/9) is the Fahrenheit-to-Centigrade factor, used in the wrong direction. It returns 87.5 °F for 100 °C instead of 212 °F. Corrected to 32 + (C x 1.8).
Millibars to inches of mercury — the original applies mbar x 0.0394, the millimetre-to-inch factor, overstating the result by about 33%. Corrected to mbar x 0.02953.

Legacy code

The original single-file minitools by Joseba Bikandi are kept verbatim in legacy/ for reference and GPL continuity. See legacy/README.md for provenance and the mapping to the modernised classes.

Tests

composer install
vendor/bin/phpunit

Licence

GNU GPL v2 only — the licence of the original BioPHP minitools.

amelaye / biotools

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