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"))