本文整理汇总了Python中process.sequence.AlignmentList.add_alignments方法的典型用法代码示例。如果您正苦于以下问题：Python AlignmentList.add_alignments方法的具体用法？Python AlignmentList.add_alignments怎么用？Python AlignmentList.add_alignments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.add_alignments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: AlignmentManipulationTest
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignments [as 别名]
class AlignmentManipulationTest(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):
try:
self.aln_obj.clear_alignments()
except:
pass
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_clear_alns(self):
self.aln_obj.clear_alignments()
aln = AlignmentList([], sql_db=sql_db)
self.assertTrue(compare_inst(self.aln_obj, aln, ["log_progression",
"locus_length",
"partitions",
"cur",
"con"]))
def test_update_act_anls(self):
self.aln_obj.update_active_alignments([join(data_path,
"BaseConc1.fas"),
join(data_path,
"BaseConc2.fas")])
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
def test_update_act_alns_err(self):
self.aln_obj.update_active_alignments([join(data_path,
"BaseConc1.fas"),
join(data_path,
"BaseConc2.fas"),
join(data_path,
"Wrong_name")])
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
def test_update_aln_shelve(self):
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"shelve")
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc2.fas"),
join(data_path, "BaseConc3.fas"),
join(data_path, "BaseConc4.fas"),
join(data_path, "BaseConc5.fas"),
join(data_path, "BaseConc6.fas"),
join(data_path, "BaseConc7.fas")])
def test_update_aln_act(self):
self.aln_obj.update_active_alignments([])
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"active")
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas")])
def test_add_aln_obj(self):
fl = self.aln_obj.alignments.keys()
aln = Alignment(dna_data_loci[0], sql_cursor=self.aln_obj.cur,
sql_con=self.aln_obj.con,
db_idx=self.aln_obj._idx + 1, temp_dir=temp_dir)
self.aln_obj.add_alignments([aln])
self.assertEqual(self.aln_obj.alignments.keys(),
fl + [join(data_path, "c97d5m4p2.loci")])
def test_remove_taxa_from_list(self):
taxa_list = [
"1285_RAD_original",
"130a_RAD_original",
"137a_RAD_original",
"1427_RAD_original",
"167a_RAD_original"
]
expected_taxa = [tx for tx in self.aln_obj.taxa_names if
tx not in taxa_list]
#.........这里部分代码省略.........