def test_RunGenovo_read_finalize_outfile(self):
"""
check if it can "read" assembled contig
TODO: have check what happen in the file format is invalid,
assuming its the correct fasta now
"""
infile_var = "fIn.fasta"
outfile_var = "fOut.fasta"
genovo = RunGenovo(infile=infile_var, outfile=outfile_var,
pdir=self.data_dir, no_iter=10, thresh=250,
check_exist=False)
result = genovo.read_outfile()
self.assertEqual(len(result), 2)
self.assertEqual(list(result.keys()), ["1", "2"])
expected = [170, 60]
for i, key in enumerate(result):
# print key, i, type(result[key]), result[key]
self.assertEqual(len(result[key]), expected[i])
