本文整理汇总了Python中process.sequence.AlignmentList类的典型用法代码示例。如果您正苦于以下问题：Python AlignmentList类的具体用法？Python AlignmentList怎么用？Python AlignmentList使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了AlignmentList类的15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: test_alternative_missing
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], "?")示例2: test_non_ascii_taxon_names
def test_non_ascii_taxon_names(self):
self.aln_obj = AlignmentList(non_ascii, sql_db=sql_db)
non_ascii_tx = [x for x in self.aln_obj.taxa_names if
x == '\xc3\xa9!"#$%&/=?\'~\xc2\xba\xc2\xaa^"><']
self.assertEqual(len(non_ascii_tx), 1)示例3: test_protein_missing_eval
def test_protein_missing_eval(self):
self.aln_obj = AlignmentList(protein_normal_missing, sql_db=sql_db)
aln = self.aln_obj.alignments.values()[0]
self.assertEqual(aln.sequence_code[1], "x")示例4: test_dna_missing_eval
def test_dna_missing_eval(self):
self.aln_obj = AlignmentList(concatenated_medium_nexus, sql_db=sql_db)
aln = self.aln_obj.alignments.values()[0]
self.assertEqual(aln.sequence_code[1], "n")示例5: test_dna_missing_default
def test_dna_missing_default(self):
self.aln_obj = AlignmentList(single_dna, sql_db=sql_db)
aln = self.aln_obj.alignments.values()[0]
self.assertEqual(aln.sequence_code[1], "n")示例6: setUp
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.reset(cur=self.aln_obj.cur,)示例7: test_single_partition
def test_single_partition(self):
self.aln_obj = AlignmentList([dna_data_fas[0]],
db_con=self.aln_obj.con,
db_cur=self.aln_obj.cur,
sql_db=sql_db)
self.assertTrue(self.aln_obj.partitions.is_single())示例8: test_non_ascii_iter_columns
def test_non_ascii_iter_columns(self):
self.aln_obj = AlignmentList(non_ascii, sql_db=sql_db)
tx_list, _, _ = next(self.aln_obj.iter_columns(include_taxa=True))
non_ascii_tx = [x for x in tx_list
if x == '\xc3\xa9!"#$%&/=?\'~\xc2\xba\xc2\xaa^"><']
self.assertEqual(len(non_ascii_tx), 1)示例9: test_non_ascii_get_taxaidx
def test_non_ascii_get_taxaidx(self):
self.aln_obj = AlignmentList(non_ascii, sql_db=sql_db)
aln = self.aln_obj.alignments.values()[0]
non_ascii_tx = [x for x in aln.taxa_idx
if x == '\xc3\xa9!"#$%&/=?\'~\xc2\xba\xc2\xaa^"><']
self.assertEqual(len(non_ascii_tx), 1)示例10: test_no_end_colon_interleave
def test_no_end_colon_interleave(self):
self.aln_obj = AlignmentList(bad_no_end_interleave, sql_db=sql_db)
aln_obj = self.aln_obj.alignments.values()[0]
data = [aln_obj.name,
aln_obj.locus_length,
len(aln_obj.taxa_idx)]
self.assertEqual(data, ["bad_no_end_interleave.nex",
898,
12])示例11: test_non_ascii_iteration
def test_non_ascii_iteration(self):
self.aln_obj = AlignmentList(non_ascii, sql_db=sql_db)
non_ascii_tx = []
for tx, _, _ in self.aln_obj.iter_alignments():
if tx == '\xc3\xa9!"#$%&/=?\'~\xc2\xba\xc2\xaa^"><':
non_ascii_tx.append(tx)
self.assertEqual(len(non_ascii_tx), 1)示例12: test_bad_wrong_size_nexus
def test_bad_wrong_size_nexus(self):
self.aln_obj = AlignmentList(bad_wrong_size, sql_db=sql_db)
aln_obj = self.aln_obj.alignments.values()[0]
data = [aln_obj.name,
aln_obj.locus_length,
len(aln_obj.taxa_idx)]
self.assertEqual(data, ["bad_wrong_size.nex",
898,
12])示例13: test_bad_file_removal_from_db
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)示例14: test_concat_custom_fileset_from_phy_partfile
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15: test_import_new_partscheme
def test_import_new_partscheme(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(concatenated_medium_nexus,
sql_db=sql_db)
self.aln_obj.partitions.reset()
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, ["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"])