def info(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
if args.select_all:
testsuites = load_testsuites(testsuite_paths, testsuite_paths.keys())
else:
testsuites = load_testsuites(testsuite_paths, args.select or [])
print('version=' + VERSION)
testsuites_descr = []
tbp = tests = 0
for name, testsuite in testsuites.items():
bp = 0
for test in testsuite.tests:
if isinstance(test.template, genes.DynamicTemplate):
bp += len(test.template.seq(spacing=args.spacing))
else:
bp += len(test.template.seq())
testsuites_descr.append('%s-%s[%d:%dbp]' % (
name, testsuite.version, len(testsuite.tests), bp))
tbp += bp
tests += len(testsuite.tests)
print('testsuites=' + ','.join(testsuites_descr))
print('sum=%d tests,%dbp' % (tests, tbp))
print('sys.prefix=' + sys.prefix)
def scan(args):
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
if args.select_all:
testsuites = load_testsuites(testsuite_paths, testsuite_paths.keys())
else:
testsuites = load_testsuites(testsuite_paths, args.select)
if not testsuites:
sys.stderr.write('\n*** you must specify at least one testsuite! ***\n\n')
sys.stderr.write('(use the -t command line switch)\n\n')
sys.exit(ERROR_COMMAND_LINE_SWITCH)
# prepare scanning {{{2
try:
fastq = Fastq(args.fastq, paired=not args.no_paired, variant=args.variant)
except FastqFileFormatException, e:
lo.error('cannot open file %s : %s'%(args.fastq, str(e)))
sys.exit(ERROR_FASTQ_FORMAT_ERROR)
def setUpClass(cls):
lo.setLevel(logging.WARNING)
cls.testsuite_paths = discover_testsuites([testsuites_alt])
cls.testsuites = load_testsuites(cls.testsuite_paths, ['MTBC'])