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(self):
design = "./data/small_for_test/design.tsv"
mat = "./data/small_for_test/matrix.tsv"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.MATRIX = mat
args.L2FC = 0.3
args.LOG = True
with captured_output() as (out, err):
tp.main_pred(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 -> header")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[1], "2.8047472709397807",
"Test fail: test_pred -> L2FC")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[2], "1.0",
"Test fail: test_pred -> KERNEL_MCC")
selected_line = all_lines[8].split("\t")
self.assertEqual(selected_line[2], "nan",
"Test fail: test_pred -> NaN")
selected_line = all_lines[3].split("\t")
self.assertEqual(
selected_line[2], "0.7856583920412332",
"Test fail: test_pred -> feature without missing value")
selected_line = all_lines[4].split("\t")
self.assertEqual(selected_line[2], "0.5833333333333334",
"Test fail: test_pred -> feature with missing value")
selected_line = all_lines[5].split("\t")
self.assertEqual(
selected_line[2], "nan",
"Test fail: test_pred -> feature too much missing value")
def test_pred_pvalue(self):
design = "./data/small_for_test/design.tsv"
mat = "./data/small_for_test/matrix.tsv"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.MATRIX = mat
args.L2FC = 0.3
args.LOG = True
args.UTEST = True
args.TTEST = True
args.FULL = True
args.AUC = True
with captured_output() as (out, err):
tp.main_pred(args, None)
output = out.getvalue()
all_lines = output.split("\n")
selected_line = all_lines[0].split("\t")
self.assertEqual(selected_line[9], "auc",
"Test fail: test_pred_pvalue -> AUC")
self.assertEqual(selected_line[10], "u_pv",
"Test fail: test_pred_pvalue -> UTEST")
self.assertEqual(selected_line[11], "t_pv",
"Test fail: test_pred_pvalue -> TTEST")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[9], "1.0",
"Test fail: test_pred_pvalue -> AUC value l1")
self.assertEqual(selected_line[10], "0.004771821713797114",
"Test fail: test_pred_pvalue -> UTEST value l1")
self.assertEqual(selected_line[11], "1.9629755742218275e-05",
"Test fail: test_pred_pvalue -> TTEST value l1")
selected_line = all_lines[8].split("\t")
self.assertEqual(selected_line[9], "nan",
"Test fail: test_pred_pvalue -> AUC value l8")
self.assertEqual(selected_line[10], "nan",
"Test fail: test_pred_pvalue -> UTEST value l8")
self.assertEqual(selected_line[11], "nan",
"Test fail: test_pred_pvalue -> TTEST value l8")
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")
def test_pred_rna_cpm(self):
design = "./data/small_for_test/design.tsv"
mat = "./data/small_for_test/matrix.tsv"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.MATRIX = mat
args.LOG = True
args.L2FC = 0.3
args.CPM = 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")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[1], "2.764979565971643",
"Test fail: test_pred_rna_cpm -> L2FC with CPM")
def test_pred_thread(self):
design = "./data/small_for_test/design.tsv"
mat = "./data/small_for_test/matrix.tsv"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.MATRIX = mat
args.L2FC = 0.3
args.LOG = True
args.THREAD = 2
with captured_output() as (out, err):
tp.main_pred(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_thread normal -> header")
selected_line = all_lines[1].split("\t")
self.assertEqual(selected_line[1], "2.8047472709397807",
"Test fail: test_pred -> L2FC")
def test_pred_all_predictive_score(self):
design = "./data/small_for_test/design.tsv"
mat = "./data/small_for_test/matrix.tsv"
args = Namespace(**vars(default_args))
args.DESIGN = design
args.MATRIX = mat
args.L2FC = 0.3
args.LOG = True
args.PPV = True
args.NPV = True
args.TPR = True
args.TNR = True
args.FNR = True
args.FPR = True
args.FDR = True
args.FOR = True
args.TS = True
args.ACC = True
args.F1 = True
with captured_output() as (out, err):
tp.main_pred(args, None)
output = out.getvalue()
all_lines = output.split("\n")
selected_line = all_lines[0].split("\t")
self.assertEqual(selected_line[5], "kernel_ppv",
"Test fail: test_pred_all_predictive_score -> PPV")
self.assertEqual(selected_line[8], "kernel_npv",
"Test fail: test_pred_all_predictive_score -> NPV")
self.assertEqual(selected_line[11], "kernel_tpr",
"Test fail: test_pred_all_predictive_score -> TPR")
self.assertEqual(selected_line[14], "kernel_tnr",
"Test fail: test_pred_all_predictive_score -> TNR")
self.assertEqual(selected_line[17], "kernel_fnr",
"Test fail: test_pred_all_predictive_score -> FNR")
self.assertEqual(selected_line[20], "kernel_fpr",
"Test fail: test_pred_all_predictive_score -> FPR")
self.assertEqual(selected_line[23], "kernel_fdr",
"Test fail: test_pred_all_predictive_score -> FDR")
self.assertEqual(selected_line[26], "kernel_for",
"Test fail: test_pred_all_predictive_score -> FOR")
self.assertEqual(selected_line[29], "kernel_ts",
"Test fail: test_pred_all_predictive_score -> TS")
self.assertEqual(selected_line[32], "kernel_acc",
"Test fail: test_pred_all_predictive_score -> ACC")
self.assertEqual(selected_line[35], "kernel_f1",
"Test fail: test_pred_all_predictive_score -> F1")
selected_line = all_lines[3].split("\t")
self.assertEqual(
selected_line[5], "0.8492063492063492",
"Test fail: test_pred_all_predictive_score -> PPV value l3")
self.assertEqual(
selected_line[8], "0.9444444444444444",
"Test fail: test_pred_all_predictive_score -> NPV value l3")
self.assertEqual(
selected_line[11], "0.9444444444444444",
"Test fail: test_pred_all_predictive_score -> TPR value l3")
self.assertEqual(
selected_line[14], "0.8333333333333331",
"Test fail: test_pred_all_predictive_score -> TNR value l3")
self.assertEqual(
selected_line[17], "0.05555555555555555",
"Test fail: test_pred_all_predictive_score -> FNR value l3")
self.assertEqual(
selected_line[20], "0.16666666666666666",
"Test fail: test_pred_all_predictive_score -> FPR value l3")
self.assertEqual(
selected_line[23], "0.15079365079365076",
"Test fail: test_pred_all_predictive_score -> FDR value l3")
self.assertEqual(
selected_line[26], "0.05555555555555555",
"Test fail: test_pred_all_predictive_score -> FOR value l3")
self.assertEqual(
selected_line[29], "0.8095238095238095",
"Test fail: test_pred_all_predictive_score -> TS value l3")
self.assertEqual(
selected_line[32], "0.8888888888888888",
"Test fail: test_pred_all_predictive_score -> ACC value l3")
self.assertEqual(
selected_line[35], "0.8931623931623932",
"Test fail: test_pred_all_predictive_score -> F1 value l3")
selected_line = all_lines[8].split("\t")
self.assertEqual(
selected_line[5], "nan",
"Test fail: test_pred_all_predictive_score -> PPV value l8")
self.assertEqual(
selected_line[8], "nan",
"Test fail: test_pred_all_predictive_score -> NPV value l8")
self.assertEqual(
selected_line[11], "nan",
"Test fail: test_pred_all_predictive_score -> TPR value l8")
self.assertEqual(
selected_line[14], "nan",
"Test fail: test_pred_all_predictive_score -> TNR value l8")
self.assertEqual(
selected_line[17], "nan",
"Test fail: test_pred_all_predictive_score -> FNR value l8")
self.assertEqual(
selected_line[20], "nan",
"Test fail: test_pred_all_predictive_score -> FPR value l8")
self.assertEqual(
selected_line[23], "nan",
"Test fail: test_pred_all_predictive_score -> FDR value l8")
self.assertEqual(
selected_line[26], "nan",
"Test fail: test_pred_all_predictive_score -> FOR value l8")
self.assertEqual(
selected_line[29], "nan",
"Test fail: test_pred_all_predictive_score -> TS value l8")
self.assertEqual(
selected_line[32], "nan",
"Test fail: test_pred_all_predictive_score -> ACC value l8")
self.assertEqual(
selected_line[35], "nan",
"Test fail: test_pred_all_predictive_score -> F1 value l8")