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])