本文整理汇总了Python中process.sequence.AlignmentList.filter_min_taxa方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentList.filter_min_taxa方法的具体用法？Python AlignmentList.filter_min_taxa怎么用？Python AlignmentList.filter_min_taxa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_min_taxa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: AlignmentTaxaFilters
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import filter_min_taxa [as 别名]
class AlignmentTaxaFilters(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_filter_min_taxa(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_min_taxa(50)
self.assertEqual(len(self.aln_obj.alignments), 5)
def test_filter_min_taxa_max(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_min_taxa(100)
self.assertEqual(len(self.aln_obj.alignments), 1)
def test_filter_min_taxa_min(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_min_taxa(0)
self.assertEqual(len(self.aln_obj.alignments), 7)
def test_filter_by_taxa_include(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_by_taxa(["spa", "spb", "spc", "spd"], "Contain")
self.assertEqual(len(self.aln_obj.alignments), 2)
def test_filter_by_taxa_exclude(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_by_taxa(["spa", "spb", "spc", "spd"], "Exclude")
self.assertEqual(len(self.aln_obj.alignments), 5)
def test_filter_by_taxa_all(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_by_taxa(["no_taxa"], "Contain")
self.assertEqual(len(self.aln_obj.alignments), 0)
def test_filter_by_taxa_from_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.filter_by_taxa("trifusion/tests/data/filter_taxa.txt",
"Contain")
self.assertEqual(len(self.aln_obj.alignments), 2)