def test_with_matching_read(self): logger = logging.getLogger(__name__) logger.setLevel(logging.ERROR) fasta = Fasta(logger, os.path.join(data_dir, 'plasmid_data.fa'), 11, True) fastq = Fastq(logger, os.path.join(data_dir, 'query.fastq'), 11, fasta.all_kmers_in_file(), 1, 50, None, None, fasta, True) self.assertTrue( fastq.does_read_contain_quick_pass_kmers( "ATCAATACCTTCTTTATTGATTTTGATATTCACACGGCAAAAGAAACTATTTCAGCAAGCGATA" "ATTTTAACAACCGCTATTGATTTAGGTTTTATGCCTACTATGATTATCAAATCTGATAAAGGTT" "ATCAAGCATATTTTGTTTTAGAAACGCCAGTCTATGTGACTTCAAAATCAGAATTTAAATCTGT" "CAAAGCAGCCAAAATAATTTCGCAAAATATCCGAGAATATTTTGGAAAGTCTTTGCCAGTTGAT" "CTAACGTGTAATCATTTTGGTATTGCTCGCATACCAAGAACGGACAATGTAGAATTTTTTGATC" "CTAATTACCGTTATTCTTTCAAAGAATGGCAAGATTGGTCTTTCAAACAAACAGATAATAAGGG" "CTTTACTCGTTCAAGTCTAACGGTTTTAAGCGGTACAGAAGGCAAAAAACAAGTAGATGAACCC" "TGGTTTAATCTCTTATTGCACGAAACGAAATTTTCAGGAGAAAAGGGTTTAATAGGGCGTAATA" "ACGTCATGTTTACCCTCTCTTTAGCCTACTTTAGTTCAGGCTATTCAATCGAAACGTGCGAATA" "TAATATGTTTGAGTTTAATAATCGATTAGATCAACCCTTAGAAGAAAAAGAAGTAATCAAAATT" "GTTAGAAGTGCCTATTCAGAAAACTATCAAGGGGCTAATAGGGAATACATTACCATTCTTTGCA" "AAGCTTGGGTATCAAGTGATTTAACCAGTAAAGATTTATTTGTCCGTCAAGGGTGGTTTAAATT" "CAAGAAAAAAAGAAGCGAACGTCAACGTGTTCATTTGTCAGAATGGAAAGAAGATTTAATGGCT" "TATATTAGCGAAAAAAGCGATGTATACAAGCCTTATTTAGTGACGACCAAAAAAGAGATTAGAG" "AAGTG"))
def test_with_nonmatching_read(self): logger = logging.getLogger(__name__) logger.setLevel(logging.ERROR) fasta = Fasta(logger, os.path.join(data_dir,'plasmid_data.fa'),4, True) fastq = Fastq(logger, os.path.join(data_dir,'query.fastq'), 4 , fasta.all_kmers_in_file(), 1, 50, None, None, fasta, True) self.assertFalse(fastq.does_read_contain_quick_pass_kmers("AAAAAAAAAAAAAAAA"))