def run(self):
try:
self.analyser.spacing = args.spacing
self.analyser.scan(fastq, testsuites, do_reverse=not args.no_reverse)
self.finished = True
except Exception, e:
self.exception = e
self.traceback = format_traceback(sys.exc_info())
def load_testsuite(fname):
"""
:param fname: path of ``.py`` testsuite file
loads a modular testsuite from a file; see :ref:`testsuites`
**beware** that the testsuite is a python file and can execute arbitrary
code
raises :py:class:`TestsuiteLoadingException` if file format of specified
testsuite is invalid
"""
name = os.path.splitext(os.path.basename(fname))[0]
if "-" in name:
name = name[: name.index("-")]
namespace = dict(__file__=fname, __module__="kvarq.testsuites." + name)
try:
sys.path.insert(0, os.path.dirname(fname))
execfile(fname, namespace)
del sys.path[0]
except Exception as e:
raise TestsuiteLoadingException(
"exception while reading file : %s [%s]" % (str(e), format_traceback(sys.exc_info()))
)
if not "GENES_COMPATIBILITY" in namespace:
raise TestsuiteLoadingException('module defines no "GENES_COMPATIBILITY"')
compat = StrictVersion(namespace["GENES_COMPATIBILITY"])
version = StrictVersion(COMPATIBILITY)
if compat > version or compat.version[0] != version.version[0]:
raise TestsuiteLoadingException("incompatible : %s needed, got %s" % (compat, version))
if not name in namespace:
raise TestsuiteLoadingException('could not import "%s"' % name)
if not isinstance(namespace[name], Testsuite):
raise TestsuiteLoadingException('modules defines "%s" but is of type %s' % type(namespace[name]))
return namespace[name]