def test_compare_ta_tss(self):
out_table = StringIO()
nums = {'pro': 3, 'tss': 3, 'uni': 0, 'cds': 3, 'ta': 3}
output = StringIO()
detects = {"overlap": False, "uni_with_tss": False}
si.get_coverage = self.mock.mock_get_coverage
args = self.mock_args.mock()
args.tex_notex = "tex_notex"
args.min_len = 30
args.max_len = 300
args.decrease_inter = 50
args.fuzzy_inter = 5
args.tolerance = 5
args.tsss = copy.deepcopy(self.example.tsss)
args.nums = nums
args.fuzzy = 20
args.detects = detects
args.texs = "texs"
args.replicates = "rep"
args.table_best = True
args.wigs_f = ""
args.wigs_r = ""
args.output = output
args.out_table = out_table
tas = copy.deepcopy(self.example.tas)
tsss = copy.deepcopy(self.example.tsss)
si.compare_ta_tss(10, 2, 15, tas[0], tsss[0], 50, "cutoff",
20, "", args)
self.assertEqual(output.getvalue(), "aaa\tANNOgesic\tsRNA\t10\t15\t.\t+\t.\tID=srna0;Name=sRNA_00000;sRNA_type=intergenic;with_TSS=TSS:170_+\n")
self.assertEqual(out_table.getvalue(), "aaa\t00000\t10\t15\t+\tNA\tNA\tNA\tNA\tNA\tTSS:170_+\n")
si.get_coverage = get_coverage
def test_compare_ta_tss(self):
out_table = StringIO()
nums = {'pro': 3, 'tss': 3, 'uni': 0, 'cds': 3, 'ta': 3}
output = StringIO()
detects = {"overlap": False, "uni_with_tss": False}
si.get_coverage = self.mock.mock_get_coverage
args = self.mock_args.mock()
args.tex_notex = "tex_notex"
args.min_len = 30
args.max_len = 300
args.decrease_inter = 50
args.fuzzy_inter = 5
args.tolerance = 5
args.tsss = copy.deepcopy(self.example.tsss)
args.nums = nums
args.fuzzy = 20
args.detects = detects
args.texs = "texs"
args.replicates = "rep"
args.table_best = True
args.wigs_f = ""
args.wigs_r = ""
args.output = output
args.out_table = out_table
tas = copy.deepcopy(self.example.tas)
tsss = copy.deepcopy(self.example.tsss)
si.compare_ta_tss(10, 2, 15, tas[0], tsss[0], 50, "cutoff", 20, "",
args)
self.assertEqual(
output.getvalue(),
"aaa\tANNOgesic\tncRNA\t10\t15\t.\t+\t.\tID=aaa_srna0;Name=sRNA_00000;sRNA_type=intergenic;with_TSS=TSS:170_+\n"
)
self.assertEqual(
out_table.getvalue(),
"aaa\t00000\t10\t15\t+\tNA\tNA\tNA\tNA\tNA\tTSS:170_+\n")
si.get_coverage = get_coverage