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Python AlignmentList.update_active_alignment方法代码示例

本文整理汇总了Python中process.sequence.AlignmentList.update_active_alignment方法的典型用法代码示例。如果您正苦于以下问题:Python AlignmentList.update_active_alignment方法的具体用法?Python AlignmentList.update_active_alignment怎么用?Python AlignmentList.update_active_alignment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process.sequence.AlignmentList的用法示例。


在下文中一共展示了AlignmentList.update_active_alignment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 update_active_alignment [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.........
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:103,代码来源:test_load_process_data.py


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