本文整理汇总了Python中process.sequence.AlignmentList.filter_segregating_sites方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentList.filter_segregating_sites方法的具体用法？Python AlignmentList.filter_segregating_sites怎么用？Python AlignmentList.filter_segregating_sites使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类process.sequence.AlignmentList的用法示例。
在下文中一共展示了AlignmentList.filter_segregating_sites方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: AlignmentVariationFilters
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import filter_segregating_sites [as 别名]
class AlignmentVariationFilters(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList([], sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_variation_filter_min(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_segregating_sites(None, None)
self.assertEqual(len(self.aln_obj.alignments), 3)
def test_variation_var_sites(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_segregating_sites(1, 2)
self.assertEqual(len(self.aln_obj.alignments), 0)
def test_variation_var_sites2(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_segregating_sites(1, 3)
self.assertEqual(len(self.aln_obj.alignments), 1)
def test_variation_inf_min(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_informative_sites(None, None)
self.assertEqual(len(self.aln_obj.alignments), 3)
def test_variation_inf_sites(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_informative_sites(1, 4)
self.assertEqual(len(self.aln_obj.alignments), 1)
def test_variation_inf_sites2(self):
self.aln_obj.add_alignment_files(variable_data)
self.aln_obj.filter_informative_sites(1, 1)
print(self.aln_obj.alignments)
self.assertEqual(len(self.aln_obj.alignments), 1)