def test_min_setting(self):
infile = self.unittest_dir + "testControlFileMin"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
print assembler.get_all_par().values()
def test_some_optional(self):
infile = self.unittest_dir + "testControlFileOp1"
setting = Setting.create_setting_from_file(infile)
assembler = SoftwareAssembler(setting)
expected = set(TestSoftwareAssembler.list_all_parameters)
self.assertEqual(expected, set(assembler.get_all_par().viewkeys()))
self.assertEqual(run_genovo.DEFAULT_GENOVO_NO_ITER, assembler.get("genovo_num_iter"))
self.assertEqual("1e-10", assembler.get("blast_e_value"))
def test_init_program(self):
setting = Setting();
setting.add_all(genovo_infile="wdir_all_reads.fa",
genovo_pdir=self.genovo_dir)
setting.add_all(glimmer_pdir=self.glimmer_dir)
setting.add_all(wdir=self.working_dir)
# setting.add_all(metasim_model_infile="ErrorModelSolexa36bp.mconf", metasim_no_reads=10, metasim_pdir=self.metasim_dir,
# metasim_taxon_infile="MetaSim_bint.mprf")
setting.add_all(mine_pdir=self.mine_dir, mine_comparison_style="-allPairs")
setting.add_all(blast_infile="dictionary", blast_e_value=1e-15, blast_wdir=self.blast_dir, blast_outfile=None)
assembly = SoftwareAssembler(setting)
assembly.init_program()
except IOError as e:
print e
# warnings.warn(e)
sys.exit(8)
# data_dir = path_utils.get_data_dir(CWD)
# print data_dir
args.debug = 2
if args.debug == 2:
print "Debug level 2"
print "All args:", args
elif args.debug == 1:
print "Debug level 1"
CWD = os.getcwd()
print "Current working directory %s" % CWD
print "NumPy version %s" % numpy.__version__
print "SciPy version %s" % scipy.__version__
print "Bio version %s at %s" % (Bio.__version__, Bio.__path__)
assembler = SoftwareAssembler.create_from_args(args)
# sys.exit(12)
assembler.run()
#
# assembler = SoftwareAssembler.create_from_args(args)
# assembler.run()
print "== END MMAP=="