def test_pred_rna_kall_trans(self):
design = "./data/small_leucegene/5_inv16_vs_5/design.tsv"
anno = "./data/small_genome/Homo_sapiens.GRCh38.84.reduce.gff3"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.N_DRAW = 10
args.LOG = True
args.CPM = True
args.ANNO = anno
args.KAL = True
with captured_output() as (out, err):
tpr.main_pred_rna(args, None)
output = out.getvalue()
all_lines = output.split("\n")
selected_line = all_lines[0].split("\t")
self.assertEqual(selected_line[2], "kernel_mcc",
"Test fail: test_pred_rna_kall_trans -> header")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[2], "0.5827131783528432",
"Test fail: test_pred_rna_kall_trans -> MCC")
def test_pred_rna_kall_gene_bagging_tpm(self):
design = "./data/small_leucegene/5_inv16_vs_5/design.tsv"
anno = "./data/small_genome/Homo_sapiens.GRCh38.84.reduce.gff3"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.BS = 5
args.LOG = True
args.N_DRAW = 10
args.N_BAGGING = 10
args.TPM = True
args.ANNO = anno
args.GENE = True
args.KAL = True
with captured_output() as (out, err):
tpr.main_pred_rna(args, None)
output = out.getvalue()
all_lines = output.split("\n")
selected_line = all_lines[1].split("\t")
self.assertEqual(
selected_line[1], "2.320041910153135",
"Test fail: test_pred_rna_kall_gene_bagging_tpm -> L2FC TPM")
def test_pred_rna_kall_miss_anno(self):
design = "./data/small_leucegene/5_inv16_vs_5/design.tsv"
anno = "./data/small_genome/Homo_sapiens.GRCh38.84.reduce2.gff3"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.N_DRAW = 10
args.LOG = True
args.CPM = True
args.ANNO = anno
args.GENE = True
args.KAL = True
with captured_output() as (out, err):
tpr.main_pred_rna(args, None)
output = out.getvalue()
all_lines = output.split("\n")
selected_line = all_lines[len(all_lines) - 2].split("\t")
self.assertEqual(selected_line[0], "ENST00000411957",
"Test fail: test_pred_rna_kall_miss_anno -> ENST")