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_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)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)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)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)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)