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Python AlignmentList.remove_file方法代码示例

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

#.........这里部分代码省略.........
        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]

        self.aln_obj.remove_taxa(taxa_list)

        self.assertEqual(self.aln_obj.taxa_names, expected_taxa)

    def test_remove_taxa_from_file(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]

        self.aln_obj.remove_taxa(taxa_to_remove)

        self.assertEqual(self.aln_obj.taxa_names, expected_taxa)

    def test_remove_taxa_from_list_inverse(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]

        self.aln_obj.remove_taxa(taxa_list, mode="inverse")

        self.assertEqual(self.aln_obj.taxa_names, taxa_list)

    #
    # def test_retrieve_alignment(self):
    #
    #     aln = self.aln_obj.retrieve_alignment("BaseConc1.fas")
    #
    #     aln2 = Alignment(dna_data_fas[0], dest="new_one")
    #
    #     self.assertTrue(compare_inst(aln, aln2,
    #                                  ["log_progression", "locus_length",
    #                                   "_partitions"]))

    def test_concatenation(self):

        self.aln_obj.concatenate()
        self.aln_obj.write_to_file(["fasta"], output_file="test")

        with open("trifusion/tests/data/BaseConcatenation.fas") as fh1, \
                open("test.fas") as fh2:
            self.assertEqual(sorted(fh1.readlines()), sorted(fh2.readlines()))

        os.remove("test.fas")

    def test_concatention_after_removal(self):

        fl = [x for x in self.aln_obj.alignments][3:]
        self.aln_obj.remove_file(fl)

        self.aln_obj.concatenate()

        self.assertEqual(len(self.aln_obj.alignments), 1)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:104,代码来源:test_load_process_data.py


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