本文整理汇总了Python中process.sequence.AlignmentList.update_active_alignments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_alignments方法的具体用法？Python AlignmentList.update_active_alignments怎么用？Python AlignmentList.update_active_alignments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类process.sequence.AlignmentList的用法示例。
在下文中一共展示了AlignmentList.update_active_alignments方法的3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: PartitonsTest
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import update_active_alignments [as 别名]
#.........这里部分代码省略.........
key_data = [self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]]
self.assertEqual(key_data,
[['BaseConc1.fas'],
['BaseConc1.fas', 'BaseConc3.fas', 'BaseConc2.fas']])
def test_merge_and_custom_split2(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part",
[(0, 84), (85, 254)],
["one", "two"])
key_data = [self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]]
self.assertEqual(key_data,
[['BaseConc1.fas'],
['BaseConc3.fas', 'BaseConc2.fas']])
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_par[0])
self.aln_obj.update_active_alignments(
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0])
self.aln_obj.update_active_alignments(
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
示例2: SeconaryOpsTest
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import update_active_alignments [as 别名]
class SeconaryOpsTest(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):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_summary_stats_all(self):
sum_table, table_data = self.aln_obj.get_summary_stats()
self.assertEqual([sum_table, table_data],
[{'missing': '5 (0.04%)', 'taxa': 24, 'genes': 7,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '7 (1.18%)',
'seq_len': 595, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[7, 24, 595, '0 (0.0%)', 0.0, '5 (0.04%)', 1.0,
'7 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_summary_stats_one_active(self):
sum_table, table_data = self.aln_obj.get_summary_stats([
join(data_path, "BaseConc1.fas")])
self.assertEqual([sum_table, table_data],
[{'missing': '1 (0.05%)', 'taxa': 24, 'genes': 1,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '1 (1.18%)',
'seq_len': 85, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[1, 24, 85, '0 (0.0%)', 0.0, '1 (0.05%)', 1.0,
'1 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_single_aln_outlier_mdata(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_missing_data(),
{"exception": "single_alignment"})
def test_single_aln_outlier_mdata_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_missing_data_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_segregating(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_segregating_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size_sp(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize_per_species(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
#.........这里部分代码省略.........
示例3: AlignmentManipulationTest
# 需要导入模块: from process.sequence import AlignmentList [as 别名]
# 或者: from process.sequence.AlignmentList import update_active_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.........