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Package biotools
Short Description Symfony forms and services for the BioPHP minitools
License GPL-2.0-only
Homepage https://www.amelayes-biophp.net
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Informations about the package biotools
BioTools
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 toapi.amelayes-biophp.net(the API adapters fetch reference data over HTTP)
Installation
Register both bundles in config/bundles.php:
Usage
Every form type and every manager is available for autowiring. A controller only has to build the form and delegate to the manager:
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:
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:
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 to32 + (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 tombar 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
Licence
GNU GPL v2 only — the licence of the original BioPHP minitools.
All versions of biotools with dependencies
amelaye/biophp Version ^2.0.1
symfony/config Version ^7.4
symfony/dependency-injection Version ^7.4
symfony/form Version ^7.4
symfony/http-foundation Version ^7.4
symfony/http-kernel Version ^7.4
symfony/options-resolver Version ^7.4
symfony/validator Version ^7.4
twig/twig Version ^3.0