本文整理汇总了Python中Bio.SearchIO.index_db方法的典型用法代码示例。如果您正苦于以下问题：Python SearchIO.index_db方法的具体用法？Python SearchIO.index_db怎么用？Python SearchIO.index_db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Bio.SearchIO的用法示例。
在下文中一共展示了SearchIO.index_db方法的4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: check_raw
# 需要导入模块: from Bio import SearchIO [as 别名]
# 或者: from Bio.SearchIO import index_db [as 别名]
def check_raw(self, filename, id, raw, **kwargs):
"""Index filename using keyword arguments, check get_raw(id)==raw."""
idx = SearchIO.index(filename, self.fmt, **kwargs)
raw = _as_bytes(raw)
# Anticipate cases where the raw string and/or file uses different
# newline characters ~ we set everything to \n.
new = idx.get_raw(id)
self.assertTrue(isinstance(new, bytes),
"Didn't get bytes from %s get_raw" % self.fmt)
self.assertEqual(raw.replace(b'\r\n', b'\n'),
new.replace(b'\r\n', b'\n'))
idx.close()
# Now again, but using SQLite backend
if sqlite3:
idx = SearchIO.index_db(":memory:", filename, self.fmt, **kwargs)
new = idx.get_raw(id)
self.assertTrue(isinstance(new, bytes),
"Didn't get bytes from %s get_raw" % self.fmt)
self.assertEqual(raw.replace(b'\r\n', b'\n'),
new.replace(b'\r\n', b'\n'))
idx.close()
if os.path.isfile(filename + ".bgz"):
# Do the tests again with the BGZF compressed file
print("[BONUS %s.bgz]" % filename)
self.check_raw(filename + ".bgz", id, raw, **kwargs)示例2: check_index
# 需要导入模块: from Bio import SearchIO [as 别名]
# 或者: from Bio.SearchIO import index_db [as 别名]
def check_index(self, filename, format, **kwargs):
# check if Python3 installation has sqlite3
try:
import sqlite3
except ImportError:
sqlite3 = None
parsed = list(SearchIO.parse(filename, format, **kwargs))
# compare values by index
indexed = SearchIO.index(filename, format, **kwargs)
self.assertEqual(len(parsed), len(indexed.keys()))
# compare values by index_db, only if sqlite3 is present
if sqlite3 is not None:
db_indexed = SearchIO.index_db(':memory:', [filename], format, **kwargs)
self.assertEqual(len(parsed), len(db_indexed.keys()))
for qres in parsed:
idx_qres = indexed[qres.id]
# parsed and indexed qresult are different objects!
self.assertNotEqual(id(qres), id(idx_qres))
# but they should have the same attribute values
self.assertTrue(compare_search_obj(qres, idx_qres))
# sqlite3 comparison, only if it's present
if sqlite3 is not None:
dbidx_qres = db_indexed[qres.id]
self.assertNotEqual(id(qres), id(dbidx_qres))
self.assertTrue(compare_search_obj(qres, dbidx_qres))
indexed._proxy._handle.close() # TODO - Better solution
if sqlite3 is not None:
db_indexed.close()
db_indexed._con.close()示例3: check_index
# 需要导入模块: from Bio import SearchIO [as 别名]
# 或者: from Bio.SearchIO import index_db [as 别名]
def check_index(self, filename, format, **kwargs):
# check if Python3 installation has sqlite3
try:
import sqlite3
except ImportError:
sqlite3 = None
if filename.endswith(".bgz"):
handle = gzip.open(filename)
parsed = list(SearchIO.parse(handle, format, **kwargs))
handle.close()
else:
parsed = list(SearchIO.parse(filename, format, **kwargs))
# compare values by index
indexed = SearchIO.index(filename, format, **kwargs)
self.assertEqual(len(parsed), len(indexed),
"Should be %i records in %s, index says %i"
% (len(parsed), filename, len(indexed)))
# compare values by index_db, only if sqlite3 is present
if sqlite3 is not None:
db_indexed = SearchIO.index_db(':memory:', [filename], format, **kwargs)
self.assertEqual(len(parsed), len(db_indexed),
"Should be %i records in %s, index_db says %i"
% (len(parsed), filename, len(db_indexed)))
for qres in parsed:
idx_qres = indexed[qres.id]
# parsed and indexed qresult are different objects!
self.assertNotEqual(id(qres), id(idx_qres))
# but they should have the same attribute values
self.assertTrue(compare_search_obj(qres, idx_qres))
# sqlite3 comparison, only if it's present
if sqlite3 is not None:
dbidx_qres = db_indexed[qres.id]
self.assertNotEqual(id(qres), id(dbidx_qres))
self.assertTrue(compare_search_obj(qres, dbidx_qres))
indexed.close()
if sqlite3 is not None:
db_indexed.close()
db_indexed._con.close()
if os.path.isfile(filename + ".bgz"):
# Do the tests again with the BGZF compressed file
print("[BONUS %s.bgz]" % filename)
self.check_index(filename + ".bgz", format, **kwargs)示例4: check_raw
# 需要导入模块: from Bio import SearchIO [as 别名]
# 或者: from Bio.SearchIO import index_db [as 别名]
def check_raw(self, filename, id, raw, **kwargs):
"""Index filename using **kwargs, check get_raw(id)==raw."""
idx = SearchIO.index(filename, self.fmt, **kwargs)
raw = _as_bytes(raw)
self.assertEqual(raw, idx.get_raw(id))
idx.close()
#Now again, but using SQLite backend
if sqlite3:
idx = SearchIO.index_db(":memory:", filename, self.fmt, **kwargs)
self.assertEqual(raw, idx.get_raw(id))
idx.close()
if os.path.isfile(filename + ".bgz"):
#Do the tests again with the BGZF compressed file
print "[BONUS %s.bgz]" % filename
self.check_raw(filename + ".bgz", id, raw, **kwargs)