def test_stap_aureus_pacbio(self):
logger = logging.getLogger(__name__)
kmer = 11
pr = cProfile.Profile()
pr.enable()
fastas = Fastas(logger, databases + '/Staphylococcus_aureus/', kmer,
False)
mlst_profile = MlstProfile(databases +
'/Staphylococcus_aureus/profile.txt')
fastq = Fastq(logger,
os.path.join(data_dir, 'NCTC11150.fastq.gz'),
kmer,
fastas.get_fastas_to_kmers(),
10,
mlst_profile,
50,
None,
None,
max_kmers=1)
self.assertTrue(fastq.read_filter_and_map())
pr.disable()
s = io.StringIO()
sortby = 'cumulative'
ps = pstats.Stats(pr, stream=s).sort_stats(sortby)
ps.print_stats()
print(s.getvalue())
def test_salmonella_welt_pacbio(self):
logger = logging.getLogger(__name__)
kmer = 11
fastas = Fastas(logger, data_dir, kmer, False)
mlst_profile = MlstProfile(data_dir + '/profile.txt')
fastq = Fastq(logger, os.path.join(data_dir, 'pacbio.fastq.gz'), kmer,
fastas.get_fastas_to_kmers(), 10, mlst_profile, 50, None,
None)
self.assertTrue(fastq.read_filter_and_map())
def test_four_kmers(self):
logger = logging.getLogger(__name__)
fastas = Fastas(logger, data_dir, 4, False)
mlst_profile = MlstProfile(data_dir + '/profile.txt')
fastq = Fastq(logger, os.path.join(data_dir, 'query.fastq'), 4,
fastas.get_fastas_to_kmers(), 1, mlst_profile, 50, None,
None)
self.assertTrue(fastq.read_filter_and_map())
def test_kp_nanopore(self):
logger = logging.getLogger(__name__)
kmer = 11
fastas = Fastas(logger, databases + '/Klebsiella_pneumoniae/', kmer,
False)
mlst_profile = MlstProfile(databases +
'/Klebsiella_pneumoniae/profile.txt')
fastq = Fastq(logger, os.path.join(data_dir,
'nanopore_kp_12.fastq.gz'), kmer,
fastas.get_fastas_to_kmers(), 10, mlst_profile, 50, None,
None)
self.assertTrue(fastq.read_filter_and_map())
def run(self):
mlst_profile = MlstProfile(self.mlst_profile_file())
fastas = Fastas(self.logger, self.allele_directory, self.kmer,
self.divisible_by_3)
fastq = Fastq(self.logger,
self.input_fastq,
self.kmer,
fastas.get_fastas_to_kmers(),
self.min_fasta_hits,
mlst_profile,
self.print_interval,
self.output_file,
self.filtered_reads_file,
target_st=self.target_st,
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)
fastq.read_filter_and_map()
def test_four_kmers(self):
logger = logging.getLogger(__name__)
f = Fastas(logger, data_dir, 4, False)
self.assertEqual(list(f.fastas_to_kmers.values()), [{
'CTGA': 1,
'TGAC': 1,
'GACG': 1,
'ACGC': 2,
'CGCC': 1,
'GCCA': 1,
'CCAA': 1,
'CAAG': 1,
'AAGG': 1,
'AGGT': 1,
'GGTG': 1,
'GTGG': 1,
'TGGC': 1,
'GGCG': 1,
'GCGG': 2,
'CGGA': 1,
'GGAG': 1,
'GAGG': 1,
'AGGC': 1,
'TTCG': 1,
'TCGT': 1,
'CGTC': 2,
'GTCG': 1,
'TCGC': 1,
'CGCG': 1,
'CGGC': 1,
'GGCT': 1,
'GCAA': 1,
'CAAC': 1,
'AACG': 1,
'CGCT': 1,
'GCTA': 1,
'CTAA': 1,
'TAAC': 1,
'ACGT': 1,
'GTCA': 1
}, {
'CTGA': 2,
'TGAC': 2,
'GACG': 1,
'ACGC': 1,
'CGCC': 1,
'GCCG': 1,
'CCGG': 1,
'CGGA': 1,
'GGAT': 1,
'GATG': 1,
'ATGC': 1,
'TGCT': 1,
'GCTG': 1,
'GACA': 1,
'ACAA': 1,
'CAAC': 1,
'AACT': 1,
'ACTG': 1,
'CTGG': 1,
'TGGC': 1,
'TTCG': 1,
'TCGT': 1,
'CGTC': 1,
'GTCG': 1,
'TCGC': 1,
'CGCT': 1,
'GCTT': 1,
'CTTC': 1,
'TTCT': 1,
'TCTG': 1,
'GACC': 1,
'ACCT': 1,
'CCTC': 1,
'CTCC': 1,
'TCCC': 1,
'CCCA': 1,
'CCAG': 1,
'CAGG': 1,
'AGGT': 1,
'GGTG': 1,
'GTGA': 1,
'TGAT': 1,
'GATC': 1,
'ATCC': 1,
'TCCT': 1,
'GCAA': 1,
'CAAT': 1,
'AATT': 1,
'ATTG': 1,
'TTGC': 1,
'TGCC': 1,
'GCCC': 1,
'CCCT': 1,
'CCTT': 1,
'CTTT': 1,
'TTTC': 1,
'TTCA': 1
}])