Added tests for validate_fasta_sequence.

tests/ValidateFastaTest.php

@@ -0,0 +1,149 @@
+<?php
+namespace Tests;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class ValidateFastaTest extends TripalTestCase {
+  // Uncomment to auto start and rollback db transactions per test method.
+  // use DBTransaction;
+
+  /**
+   * Test validate_fasta_sequence() detects invalid sequence.
+   *
+   * @dataProvider provideInvalidFasta
+   */
+  public function testInvalidFasta($type, $sequence) {
+    $this->assertFalse(validate_fasta_sequence($type, $sequence),
+      "Failed to detect invalid FASTA sequence.");
+  }
+
+  /**
+   * Test validate_fasta_sequence() works for valid sequence.
+   *
+   * @dataProvider provideValidFasta
+   */
+  public function testValidFasta($type, $sequence) {
+    $this->assertTrue(validate_fasta_sequence($type, $sequence),
+      "Unable to pass valid fasta sequence");
+  }
+
+  /**
+   * Provide invalid fasta entries to test.
+   */
+  public function provideInvalidFasta() {
+    return [
+      ['nucleotide',
+'>good first record
+ATCGACTAGCTACGATCGACTAGCAGTCAGTACTGACGTACTACGATCGACTAGCATGCT
+GCATCGATCGATCGACTATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGACT
+> space before definition
+ATTTGGGTGGTTGGGGTTCCCCCACACCGTGGGGTTTGGCAAAACCCGTGGGGCCACACA
+CACACCCCTGGGGTGTGACCCGTAACGCGAATATGCGCGATATTACGGCGCGCGATATTA'
+      ],
+      ['nucleotide',
+'>Has incorrect characters
+ACGTGCATGCATCGACACTACGACTACGACTACTAGCTCGACTGATCGACATCGATCGAT
+ACGTCAGCTACGGCGCGGCATGATCGAZZZZZZZZZZZZZZZZZZTCGCAACCCCTTTCA'
+      ],
+      ['nucleotide',
+'>Has special characters
+AACGTACGATCGACTAGCTACGATCGATCGACTAGCTAGCATCGATCGATCGATCGATCG
+AATTGTCAACGT%%#^&^&%%$$#@@!#%^&*()@ACACGTAGCTAGGCCAACGTGCAAA'
+      ],
+      ['nucleotide',
+'>Has numbers
+ACGTACGATCGATCGACTAGCTAGCATCGATCGATCGATCAGCATCGATCGATCGACTCG
+ACGTACGATCGATCGA2425345345ACGATCGACTAGCTAGCATCGATCGATCAGTCAG'
+      ],
+      ['protein', 
+'>good first record
+ACGTURYKMSWBDACGTURYKMSWBDHACGTURYKMSWBDHVNXACGTURYKMSWBDHVNXVNXHVNX
+ACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHVACGTURYKMSWBDHVNXNXXX
+> space before identifier
+ACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHVACGTURYKMSWBDHVNXNXXX
+ACGTURYKMSWBDHVNACGTACGTURYKMACGTURYKMSWBDHVNXSWBDHVNXURYKMSWBDHVNXX'
+      ],
+      ['protein', 
+'>Has incorrect characters
+ACGTURYKMSWBDACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHVNXXXHVNX
+ACGTURYKMSWBDHVACGTURYKMSWBZZZZZZZZZZZZZZZZZZDHVNACGTURYKMSWBDHVNXNZ'
+      ],
+      ['protein', 
+'>Has special characters
+ACGTURYKMSACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHVNXXXWBDHVNX
+ACGTURYKMSWBACGTURYKMSWB%#$%#$%#$^$%^%&^%&*&(*)()(!!#@#$#^DHVNXDHVNX'
+      ],
+      ['protein', 
+'>Has numbers
+ACGTURYKMSWBDHVACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHVNXXXNX
+ACGTURYKMSWACGTURYKMSWB13212324ACGTURYKMSWBDHVNX324443556DHVNXBDHVNX'
+      ],
+    ];
+  }
+
+  /**
+   * Provide Valid FASTA entries to test.
+   */
+  public function provideValidFasta() {
+    return [
+      ['nucleotide',
+'>identifier description
+ACGACTGTACGCGAGCTACGTACGTAGCATGCATCGATCGATCGATCGATCGATCGATC
+AGCTAGTCAGCATCGATGCATGCATCGACGTAATCGAGCGTAGCGAGCTAGTCATACGT'
+      ],
+      ['nucleotide',
+'>identifier
+ACGTACGATCGATCGATCGATCGATCGATCGACATGCTACGATCGATCGATCGATCGG'
+      ],
+      ['nucleotide',
+'>mutlifasta description
+AGCTAGCATCGATCGATCAGCTAGCATCGATCGATCGACTAGCTAGCATCGATCGATC
+CGATCGATCAGCTAGCTACGATCGATCGATCGATCGACTAGCTACGATCGATCGATCG
+CGATCGACTAGCGTACGATCGATCGATCGATCGATCGATCGATCACGATCAGCTACGT
+>multifasta description
+GCTACGATCGATCAGCTATCGACTATCGACGTATCGATGGAGTCATGCAGTCATGCAG
+ACGCTACGATCAGCGTACGATCGATCGATCGATCGATCGATCGATCGATCGGTGCGTC'
+      ],
+      ['nucleotide',
+'>with spaces in sequence
+ACGATCGATCGATCGATAGCTACGATCGATCGATCGATCAGCTAGCTACGATCGATCA
+ACAGCATCAGCTAG ACGATCAGCTAGCTACGATCGATCG  ACTGATCAGCATGCAT
+AACGTACGATCAGCTAGCATGCAT   ATCGATCAGCTAGCTACGATCGATCGATCAG'
+      ],
+      ['nucleotide',
+'>masked sequence
+acgatcgatcgactagctacgatcgacatcgatcatgAACGTGTGGGGTGTGTGCAa
+cagctagctagcatcgatcgatcgatcagctagcatgctacgagtcagcatcgtgca'
+      ],
+      ['protein',
+'>identier description
+ACGTURYKMSWBDHACGTURYKACGTURYKMSWBACGTURYKNXMSWBDHVNXVNX
+YKMSWACGTURYKMSWBDHVNXBDHVNXACGTURYACGTURYKMSWBDSWBDHATK'
+      ],
+      ['protein',
+'>identifier
+ACGTURYKMSWBACGTURYKMSWBDHVNXDACGTURYKMSWBDHVNXHVACGTURY
+ACGTURYKMSWBDHVNACGTURYKMSWBDACGTURYKMSWBDHVNXHVACGTURXX'
+      ],
+      ['protein',
+'>multifasta description
+ACGTURYKMSWBDHVNACGTURYKMSWBDHVNACGTURYKMSWBDHACGTURYKMSWBDHVNXVNXXX
+ACGTURYKMSWBDACGTURYKMSWBACGTURYKMSWBDHACGTURYKMSWBDHVNXVNXDHVNXHVNX
+>multifasta description
+ACGTURYKMSWBACGTURYKMSWBDHVNACGTURYKMSWBDHVACGTURYKMSWBDHVNXNXXDHVNX
+ACGTURYKMSWBDHVNACGTURYKMSACGTURYKMSWBDACGTURYKMSWBDHVNXHVNXWBDHVNXX'
+      ],
+      ['protein',
+'>with spaces in sequence
+ACGTURYKMSWBDACGTURY KMSWBDHACGTURYKMSWBDH VACGTURYKMSW   BDHVNXNXVNXHVNX
+ ACACGTURYKMSWBDHVGTURY  K MSWBDHVNX ACGTURYKMSWBDH  VACGTURYKMSWBDHVNXNX'
+      ],
+      ['protein',
+'>masked sequence
+acgturykmswbdhvacgturykmswbdhvacgturykmswbdhvnacgturykmswbdhAXNvnxxnxnx
+acgturykmswbacgturykmswbdhvnxacgtuTTUrykmswbdhvnxdacgturykmswbdhvnxhvnx'
+      ]
+    ];
+  } 
+}