def test_detect_wig_pos(self):
si.replicate_comparison = self.mock.mock_replicate_comparison
nums = {'pro': 3, 'tss': 3, 'uni': 0, 'cds': 3, 'ta': 3}
out_table = StringIO()
output = StringIO()
args = self.mock_args.mock()
args.texs = "texs"
args.replicates = "rep"
args.max_len = 300
args.min_len = 30
args.decrease_inter = 50
args.fuzzy_inter = 5
args.tex_notex = "tex_notex"
args.pros = copy.deepcopy(self.example.pros)
tas = copy.deepcopy(self.example.tas)
args.table_best = True
args.nums = nums
args.out_table = out_table
args.output = output
args.tolerance = 5
si.detect_wig_pos(self.example.wigs, tas[0], 20, 70, "TSS_160+",
10, 20, args)
self.assertEqual(output.getvalue(),
("aaa\tANNOgesic\tncRNA\t20\t190\t.\t+\t.\t"
"ID=aaa_srna0;Name=sRNA_00000;sRNA_type=intergenic;"
"with_TSS=TSS_160+;end_cleavage=Cleavage:190_+;"
"best_avg_coverage=40;best_high_coverage=50;"
"best_low_coverage=10\n"))
self.assertEqual(out_table.getvalue(),
("aaa\t00000\t20\t190\t+\tcond1\t"
"test1\t40\t50\t10\t\n"))
def test_detect_wig_pos(self):
si.replicate_comparison = self.mock.mock_replicate_comparison
nums = {'pro': 3, 'tss': 3, 'uni': 0, 'cds': 3, 'ta': 3}
out_table = StringIO()
output = StringIO()
args = self.mock_args.mock()
args.texs = "texs"
args.replicates = "rep"
args.max_len = 300
args.min_len = 30
args.decrease_inter = 50
args.fuzzy_inter = 5
args.tex_notex = "tex_notex"
args.pros = copy.deepcopy(self.example.pros)
tas = copy.deepcopy(self.example.tas)
args.table_best = True
args.nums = nums
args.out_table = out_table
args.output = output
args.tolerance = 5
si.detect_wig_pos(self.example.wigs, tas[0], 20, 70, "TSS_160+", 10,
20, args)
self.assertEqual(
output.getvalue(),
"aaa\tANNOgesic\tncRNA\t20\t190\t.\t+\t.\tID=aaa_srna0;Name=sRNA_00000;sRNA_type=intergenic;with_TSS=TSS_160+;end_cleavage=Cleavage:190_+;best_avg_coverage=40;best_high_coverage=50;best_low_coverage=10\n"
)
self.assertEqual(
out_table.getvalue(),
"aaa\t00000\t20\t190\t+\tcond1\ttest1\t40\t50\t10\t\n")