Dna sequence (#24)

* feature: Add Support Illumina NovaSeq Sample Sheets

Author: simbig

CHANGELOG.md

@@ -9,6 +9,12 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v2.2.0
+
+### Added
+
+- add `DnaSequence`-class
+
 ## v2.1.0
 
 ### Added

src/DnaSequence.php

@@ -0,0 +1,41 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils;
+
+class DnaSequence
+{
+    protected string $sequence;
+
+    public function __construct(string $sequence)
+    {
+        if (\Safe\preg_match('/^[ATGC]*$/', $sequence) === 0) {
+            throw new \InvalidArgumentException('Invalid DNA sequence');
+        }
+        $this->sequence = $sequence;
+    }
+
+    public function reverse(): string
+    {
+        return implode(array_reverse(mb_str_split($this->sequence)));
+    }
+
+    public function complement(): string
+    {
+        return $this->complementSequence($this->sequence);
+    }
+
+    public function reverseComplement(): string
+    {
+        return $this->complementSequence($this->reverse());
+    }
+
+    private function complementSequence(string $sequence): string
+    {
+        return strtr($sequence, [
+            'A' => 'T',
+            'T' => 'A',
+            'G' => 'C',
+            'C' => 'G',
+        ]);
+    }
+}

tests/DnaSequenceTest.php

@@ -0,0 +1,41 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tests;
+
+use MLL\Utils\DnaSequence;
+use PHPUnit\Framework\TestCase;
+
+class DnaSequenceTest extends TestCase
+{
+    public function testReverse(): void
+    {
+        $dnaSequence = new DnaSequence('ATGC');
+        self::assertEquals('CGTA', $dnaSequence->reverse());
+    }
+
+    public function testComplement(): void
+    {
+        $dnaSequence = new DnaSequence('ATGC');
+        self::assertEquals('TACG', $dnaSequence->complement());
+    }
+
+    public function testReverseComplement(): void
+    {
+        $dnaSequence = new DnaSequence('ATGC');
+        self::assertEquals('GCAT', $dnaSequence->reverseComplement());
+    }
+
+    public function testInvalidSequenceThrowsException(): void
+    {
+        $this->expectException(\InvalidArgumentException::class);
+        new DnaSequence('INVALID');
+    }
+
+    public function testEmptySequence(): void
+    {
+        $dnaSequence = new DnaSequence('');
+        self::assertEquals('', $dnaSequence->reverse());
+        self::assertEquals('', $dnaSequence->complement());
+        self::assertEquals('', $dnaSequence->reverseComplement());
+    }
+}