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Python AlignmentList.add_alignment_files方法代码示例

本文整理汇总了Python中process.sequence.AlignmentList.add_alignment_files方法的典型用法代码示例。如果您正苦于以下问题:Python AlignmentList.add_alignment_files方法的具体用法?Python AlignmentList.add_alignment_files怎么用?Python AlignmentList.add_alignment_files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.add_alignment_files方法的5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: LoadAlignmentsTest

# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignment_files [as 别名]

#.........这里部分代码省略.........
    def test_load_loci(self):

        self.aln_obj = AlignmentList(dna_data_loci, sql_db=sql_db)

    def test_load_single_loci(self):

        single_aln = Alignment(dna_data_loci[0], sql_cursor=self.aln_obj.cur,
                               db_idx=self.aln_obj._idx + 1)

    def test_load_nexus_par(self):

        self.aln_obj = AlignmentList(concatenated_medium_nexus, sql_db=sql_db)
        self.assertTrue(self.aln_obj.partitions.partitions)

    def test_load_wrong_type(self):

        self.aln_obj = AlignmentList(bad_file, sql_db=sql_db)
        self.assertTrue(self.aln_obj.bad_alignments)

    def test_duplicate_files(self):

        self.aln_obj = AlignmentList(dna_data_loci + dna_data_loci,
                                     sql_db=sql_db)
        self.assertTrue(self.aln_obj.duplicate_alignments)

    def test_unequal_length(self):

        self.aln_obj = AlignmentList(unequal_file, sql_db=sql_db)
        self.assertTrue(self.aln_obj.non_alignments)

    def test_bad_file_removal_from_db(self):

        self.aln_obj = AlignmentList(unequal_file, sql_db=sql_db)
        self.aln_obj.add_alignment_files(dna_data_fas)

        s = 0

        for tx, _, _ in self.aln_obj.iter_alignments():
            if tx == "Seq1":
                s += 1

        self.assertEqual(s, 0)

    def test_load_no_data(self):

        self.aln_obj = AlignmentList(no_data, sql_db=sql_db)

    def test_alternative_missing(self):

        self.aln_obj = AlignmentList(alternative_missing, sql_db=sql_db)

        aln = self.aln_obj.alignments.values()[0]

        self.assertEqual(aln.sequence_code[1], "?")

    def test_dna_missing_default(self):

        self.aln_obj = AlignmentList(single_dna, sql_db=sql_db)

        aln = self.aln_obj.alignments.values()[0]

        self.assertEqual(aln.sequence_code[1], "n")

    def test_protein_missing_default(self):

        self.aln_obj = AlignmentList(protein_no_missing, sql_db=sql_db)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:70,代码来源:test_load_process_data.py

示例2: AlignmentVariationFilters

# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignment_files [as 别名]
class AlignmentVariationFilters(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_variation_filter_min(self):

        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_segregating_sites(None, None)

        self.assertEqual(len(self.aln_obj.alignments), 3)

    def test_variation_var_sites(self):

        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_segregating_sites(1, 2)

        self.assertEqual(len(self.aln_obj.alignments), 0)

    def test_variation_var_sites2(self):
        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_segregating_sites(1, 3)

        self.assertEqual(len(self.aln_obj.alignments), 1)

    def test_variation_inf_min(self):
        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_informative_sites(None, None)

        self.assertEqual(len(self.aln_obj.alignments), 3)

    def test_variation_inf_sites(self):

        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_informative_sites(1, 4)

        self.assertEqual(len(self.aln_obj.alignments), 1)

    def test_variation_inf_sites2(self):

        self.aln_obj.add_alignment_files(variable_data)

        self.aln_obj.filter_informative_sites(1, 1)

        print(self.aln_obj.alignments)

        self.assertEqual(len(self.aln_obj.alignments), 1)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:64,代码来源:test_process_filters.py

示例3: AlignmentCodonFilters

# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignment_files [as 别名]
class AlignmentCodonFilters(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_codon_filter_pos1(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([True, False, False],
                                            table_out="master_out")

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments("master_out"):
            s.append(seq)

        self.assertEqual(s, ["a" * 16] * 10)

    def test_codon_filter_pos2(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([False, True, False],
                                            table_out="master_out")

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments("master_out"):
            s.append(seq)

        self.assertEqual(s, ["t" * 16] * 10)

    def test_codon_filter_pos3(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([False, False, True],
                                            table_out="master_out")

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments("master_out"):
            s.append(seq)

        self.assertEqual(s, ["g" * 16] * 10)

    def test_codon_filter_pos12(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([True, True, False],
                                            table_out="master_out")

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments("master_out"):
            s.append(seq)

        self.assertEqual(s, ["at" * 16] * 10)

    def test_codon_filter_pos13(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([True, False, True],
                                            table_out="master_out")

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments("master_out"):
            s.append(seq)

        self.assertEqual(s, ["ag" * 16] * 10)

    def test_codon_filter_all(self):

        self.aln_obj.add_alignment_files(codon_filter)

        self.aln_obj.filter_codon_positions([True, True, True])

        s = []
        for _, seq, _ in self.aln_obj.iter_alignments():
            s.append(seq)

        self.assertEqual(s, ["atg" * 16] * 10)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:93,代码来源:test_process_filters.py

示例4: AlignmentMissingFiltersTest

# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignment_files [as 别名]
class AlignmentMissingFiltersTest(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_default(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data.phy",
             "trifusion/tests/data/missing_data2.phy"]
        )
        self.aln_obj.filter_missing_data(25, 50)

        s = []
        for aln in self.aln_obj:
            s.append(aln.locus_length)

        self.assertEqual(s, [42, 43])

    def test_filter_and_concat(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data.phy",
             "trifusion/tests/data/missing_data2.phy"]
        )

        self.aln_obj.filter_missing_data(25, 50, table_out="master_out")

        self.aln_obj.concatenate(table_in="master_out")

        self.assertEqual(self.aln_obj.size, 85)

    def test_no_filters(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data.phy",
             "trifusion/tests/data/missing_data2.phy"]
        )

        self.aln_obj.filter_missing_data(100, 100)

        s = []
        for aln in self.aln_obj:
            s.append(aln.locus_length)

        self.assertEqual(s, [50, 50])

    def test_no_missing(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data.phy",
             "trifusion/tests/data/missing_data2.phy"]
        )
        self.aln_obj.filter_missing_data(0, 0)

        s = []
        for aln in self.aln_obj:
            s.append(aln.locus_length)

        self.assertEqual(s, [0, 19])

    def test_no_data_aln_default_filters(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data3.phy"]
        )

        self.aln_obj.filter_missing_data(25, 50)

        s = None
        for aln in self.aln_obj:
            s = aln.locus_length

        self.assertEqual(s, 0)

    def test_no_data_aln_no_filters(self):

        self.aln_obj.add_alignment_files(
            ["trifusion/tests/data/missing_data3.phy"]
        )

        self.aln_obj.filter_missing_data(100, 100)

        s = None
        for aln in self.aln_obj:
            s = aln.locus_length

        self.assertEqual(s, 50)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:100,代码来源:test_process_filters.py

示例5: AlignmentTaxaFilters

# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import add_alignment_files [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)
开发者ID:ODiogoSilva,项目名称:TriFusion,代码行数:73,代码来源:test_process_filters.py


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