本文整理汇总了Python中process.sequence.AlignmentList.outlier_missing_data_sp方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentList.outlier_missing_data_sp方法的具体用法？Python AlignmentList.outlier_missing_data_sp怎么用？Python AlignmentList.outlier_missing_data_sp使用的例子？那么恭喜您, 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.outlier_missing_data_sp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: SeconaryOpsTest
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import outlier_missing_data_sp [as 别名]
class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_summary_stats_all(self):
sum_table, table_data = self.aln_obj.get_summary_stats()
self.assertEqual([sum_table, table_data],
[{'missing': '5 (0.04%)', 'taxa': 24, 'genes': 7,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '7 (1.18%)',
'seq_len': 595, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[7, 24, 595, '0 (0.0%)', 0.0, '5 (0.04%)', 1.0,
'7 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_summary_stats_one_active(self):
sum_table, table_data = self.aln_obj.get_summary_stats([
join(data_path, "BaseConc1.fas")])
self.assertEqual([sum_table, table_data],
[{'missing': '1 (0.05%)', 'taxa': 24, 'genes': 1,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '1 (1.18%)',
'seq_len': 85, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[1, 24, 85, '0 (0.0%)', 0.0, '1 (0.05%)', 1.0,
'1 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_single_aln_outlier_mdata(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_missing_data(),
{"exception": "single_alignment"})
def test_single_aln_outlier_mdata_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_missing_data_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_segregating(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_segregating_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size_sp(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize_per_species(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
#.........这里部分代码省略.........