data_dir=self.data_dir)
vcfFile.close()
logMessage += "%s individuals, %s loci, md5sum=%s.\n" % (
no_of_individuals, no_of_loci, md5sum)
else:
logMessage += " is empty (no loci) or not VCF file.\n"
self.outputLogMessage(logMessage)
if self.commit:
try:
session.flush()
session.commit()
except:
sys.stderr.write('Except type: %s\n' % repr(sys.exc_info()))
import traceback
traceback.print_exc()
self.cleanUpAndExitOnFailure(exitCode=3)
else:
session.rollback()
#delete all target files but exit gracefully (exit 0)
self.cleanUpAndExitOnFailure(exitCode=0)
if __name__ == '__main__':
main_class = AddVCFFile2DB
po = ProcessOptions(sys.argv,
main_class.option_default_dict,
error_doc=main_class.__doc__)
instance = main_class(po.arguments, **po.long_option2value)
instance.run()
def __init__(self, **keywords):
"""
2011-7-12
"""
self.ad = ProcessOptions.process_function_arguments(keywords, self.option_default_dict, error_doc=self.__doc__, \
class_to_have_attr=self)
