def test_scan_illustrate(self):
lo.setLevel(logging.WARNING)
# do a complete scan with a known result; specify variatn
out, err = self.scan_illustrate(MTBC_fastq1,
['--variant', 'Illumina 1.8+'])
for resistance in [
'Streptomycin resistance::SNP781687AG=rpsL.K43R',
'Ethambutol resistance::SNP4247431GT=embB.M306I',
'Isoniazid resistance [2155168CG=katG.S315T]',
'Rifampicin resistance (RRDR) [761139CG=rpoB.H445D 761140AG=rpoB.H445R]',
'remark: low coverage (RRDR below 10x)']:
assert resistance in out, MTBC_fastq1 + ' should have ' + resistance
assert 'lineage 3' in out, MTBC_fastq1 + ' should be Lineage 3'
# another tested .fsatq
out, err = self.scan_illustrate(MTBC_fastq2)
for resistance in [
'Streptomycin resistance::SNP781687AG=rpsL.K43R',
'remark: low coverage (RRDR below 10x)']:
assert resistance in out, MTBC_fastq2 + ' should have ' + resistance
assert 'lineage 2' in out, MTBC_fastq2 + ' should be Lineage 2'
lo.setLevel(logging.INFO)
def test_fastq_variant(self):
lo.setLevel(logging.WARNING)
fq = self.ntf_write_quality('!"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJ');
assert fq.dQ == 0 and set(fq.variants) == set(['Illumina 1.8+', 'Sanger']), \
'FastQ variant should be Illumina 1.8+ / Sanger (dQ=0)'
fq = self.ntf_write_quality(';<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh')
assert fq.dQ == 31 and fq.variants == ['Solexa'], \
'FastQ variant should be Solexa (dQ=31)'
fq = self.ntf_write_quality('OPQRSTUVWXYZ[\]^_`abcdefgh')
assert fq.dQ == 31 and fq.variants == ['Solexa', 'Illumina 1.3+', 'Illumina 1.5+'], \
"FastQ variant should be ['Solexa', 'Illumina 1.3+', 'Illumina 1.5+'] (dQ=31)"
try:
fq = self.ntf_write_quality(';<=>?@ABCDEFGHI;<=>?@ABCDEFGHI')
raise Exception(
'Quality score ";<=>?@ABCDEFGHI" ambiguous, should not be decoded!')
except FastqFileFormatException:
pass
# specify valid vendor variants
fq = self.ntf_write_quality(';<=>?@ABCDEFGHI;<=>?@ABCDEFGHI',
variant='Sanger')
fq = self.ntf_write_quality(';<=>?@ABCDEFGHI;<=>?@ABCDEFGHI',
variant='Solexa')
# specify invalid vendor variant, must emit warning
lo_assert = lo_exceptor('seems not to be compatible', logging.WARNING, True)
fq = self.ntf_write_quality(';<=>?@ABCDEFGHI;<=>?@ABCDEFGHI',
variant='Illumina 1.3+')
lo_assert()
lo.setLevel(logging.INFO)
def scan_illustrate(self, MTBC_fastq, scan_params=[]):
ntf = tempfile.NamedTemporaryFile(delete=False)
lo.setLevel(logging.WARNING)
try:
t0 = time.time()
out, err = self.main(['scan', '-l', 'MTBC', '-f'] + scan_params + [
MTBC_fastq, ntf.name])
if time.time() - t0 > 10:
lo.warning('scanning of %s took %.2fs' % (
os.path.basename(MTBC_fastq), time.time() - t0))
out, err = self.main(['illustrate', '-r',
ntf.name])
finally:
lo.setLevel(logging.INFO)
ntf.close()
os.remove(ntf.name)
return out, err
def test_load_testsuites(self):
def get_testsuites(out):
line = [line for line in out.split('\n')
if line.startswith('testsuites=')][0]
return set([testsuite
for testsuite in line[line.index('=')+1:].split(',')
if testsuite])
def name_and_version(testsuites):
return set([testsuite[:testsuite.find('[')]
for testsuite in testsuites])
def name_only(testsuites):
return set([testsuite[:testsuite.find('-')]
for testsuite in testsuites])
cwd = os.getcwd()
out, err = self.main(['info'])
assert get_testsuites(out) == set()
# suppress "loaded testsuite" messages
lo.setLevel(logging.WARNING)
MTBC_testsuites = set(['MTBC/phylo', 'MTBC/resistance', 'MTBC/spoligo'])
# select testsuite
out, err = self.main(['info', '-l', 'MTBC/phylo'])
assert name_only(get_testsuites(out)) == set(['MTBC/phylo'])
# select group
out, err = self.main(['info', '-l', 'MTBC'])
assert name_only(get_testsuites(out)) == MTBC_testsuites
# select testsuite by filename
path = os.path.join(testsuites_alt, 'MTBC', 'phylo.py')
out, err = self.main(['info', '-l', path])
assert name_and_version(get_testsuites(out)) == set(['MTBC/phylo-0.0'])
# override testsuite directory using switch
out, err = self.main(['info', '-l', 'MTBC/phylo'])
assert name_and_version(get_testsuites(out)) != set(['MTBC/phylo-0.0'])
out, err = self.main(['-t', testsuites_alt, 'info', '-l', 'MTBC/phylo'])
assert name_and_version(get_testsuites(out)) == set(['MTBC/phylo-0.0'])
# override testsuite directory using KVARQ_TESTSUITES
os.environ['KVARQ_TESTSUITES'] = testsuites_alt
out, err = self.main(['info', '-l', 'MTBC/phylo'])
assert name_and_version(get_testsuites(out)) == set(['MTBC/phylo-0.0'])
del os.environ['KVARQ_TESTSUITES']
# time load all
t0 = time.time()
out, err = self.main(['info', '-L'])
assert len(name_only(get_testsuites(out))) > 4
if time.time() - t0 > 2:
lo.warning('loading all testsuites takes %.2f' % (time.time() - t0))
lo.setLevel(logging.INFO)
os.chdir(cwd)
def tearDownClass(cls):
lo.setLevel(logging.INFO)
def setUpClass(cls):
lo.setLevel(logging.WARNING)
cls.testsuite_paths = discover_testsuites([testsuites_alt])
cls.testsuites = load_testsuites(cls.testsuite_paths, ['MTBC'])