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()