def run(self):
self.logger.info("Starting analysis")
fasta = Fasta(self.logger,
self.plasmid_data,
self.kmer,
self.homopolyer_compression,
max_kmer_count=self.max_kmer_count)
fastq = Fastq(self.logger,
self.input_fastq,
self.kmer,
fasta.all_kmers_in_file(),
self.min_fasta_hits,
self.print_interval,
self.output_file,
self.filtered_reads_file,
fasta,
self.homopolyer_compression,
max_gap=self.max_gap,
min_block_size=self.min_block_size,
margin=self.margin,
start_time=self.start_time,
min_kmers_for_onex_pass=self.min_kmers_for_onex_pass,
min_perc_coverage=self.min_perc_coverage,
max_kmer_count=self.max_kmer_count,
no_gene_filter=self.no_gene_filter)
fastq.read_filter_and_map()
def test_gzipped_input(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_gz.fastq.gz'), 4 , fasta.all_kmers_in_file(), 1, 50, None, None, fasta, True) self.assertTrue(fastq.read_filter_and_map())
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"))
def test_filtering_alleles_partial_equal_values(self):
logger = logging.getLogger(__name__)
logger.setLevel(logging.ERROR)
fastq = Fastq(logger, os.path.join(data_dir,'query.fastq'), 11 , None, 1, 50, None, None, None, True)
input_alleles = [ Gene('rep7.1_repC(Cassette)_AB037671', 9, 1), Gene('rep7.5_CDS1(pKC5b)_AF378372', 9, 1), Gene('rep7.6_ORF(pKH1)_SAU38656', 9, 1), Gene('repUS14.1_repA(VRSAp)_AP003367', 10, 0)]
expected_allele_names = ['rep7.1','repUS14.1']
filtered_alleles = fastq.filter_contained_alleles(input_alleles)
self.assertEqual(expected_allele_names, sorted(list(map(lambda x: x.short_name(), filtered_alleles))))
def test_writting_to_output_file(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_gz.fastq.gz'), 4 , fasta.all_kmers_in_file(), 1, 50, 'outputfile', None, fasta, True)
fastq.read_filter_and_map()
self.assertTrue(os.path.exists('outputfile'))
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'expected_outputfile'), 'outputfile'))
os.remove('outputfile')