def _create_seqLenDict(self, dictpath, seqpath, reader=None):
"""Create a seqLenDict from 'seqpath' and store in 'dictpath'."""
seqLenDict = classutil.open_shelve(dictpath, 'n')
try:
logger.debug('Building sequence length index...')
_store_seqlen_dict(seqLenDict, seqpath, reader)
finally:
seqLenDict.close() # close after writing, no matter what!
return classutil.open_shelve(dictpath, 'r') # re-open read-only
def _create_seqLenDict(self, dictpath, seqpath, reader=None):
"""Create a seqLenDict from 'seqpath' and store in 'dictpath'."""
seqLenDict = classutil.open_shelve(dictpath, 'n')
try:
logger.debug('Building sequence length index...')
_store_seqlen_dict(seqLenDict, seqpath, reader)
finally:
seqLenDict.close() # close after writing, no matter what!
return classutil.open_shelve(dictpath, 'r') # re-open read-only
def __init__(self,
filename,
mode=None,
writeback=False,
unpicklingMode=False,
verbose=True,
**kwargs):
'''Wrapper for a shelve object that can be pickled. Ideally, you
should specify a TWO letter mode string: the first letter to
indicate what mode the shelve should be initially opened in, and
the second to indicate the mode to open the shelve during unpickling.
e.g. mode='nr': to create an empty shelve (writable),
which in future will be re-opened read-only.
Also, mode=None makes it first attempt to open read-only, but if the file
does not exist will create it using mode 'c'. '''
# Mark this string as a file path.
self.filename = classutil.SourceFileName(str(filename))
self.writeback = writeback
if unpicklingMode or mode is None or mode == 'r':
# Just use mode as given.
self.mode = mode
elif mode == 'n' or mode == 'c' or mode == 'w':
# Ambiguous modes, warn & set default.
if verbose:
import sys
print >> sys.stderr, '''Warning: you opened shelve file %s
in mode '%s' but this is ambiguous for how the shelve should be
re-opened later during unpickling. By default it will be
re-opened in mode 'r' (read-only). To make it be re-opened
writable, create it in mode '%sw', or call its method
reopen('w'), which will make it be re-opened in mode 'w' now and
in later unpickling. To suppress this warning message, use the
verbose=False option.''' % (filename, mode, mode)
self.mode = 'r'
else: # PROCESS UNAMBIGUOUS TWO-LETTER mode STRING
try:
if len(mode) == 2 and mode[0] in 'ncwr' and mode[1] in 'cwr':
self.mode = mode[1] # IN FUTURE OPEN IN THIS MODE
mode = mode[0] # OPEN NOW IN THIS MODE
else:
raise ValueError('invalid mode string: ' + mode)
except TypeError:
raise ValueError('file mode must be a string!')
if unpicklingMode:
self.d = classutil.open_shelve(filename,
mode,
writeback,
allowReadOnly=True)
else:
self.d = classutil.open_shelve(filename, mode, writeback)
classutil.apply_itemclass(self, kwargs)
def _init_subclass(cls, db, filepath, **kwargs):
'''initialize our indexes if needed, and provide db with a
seqInfoDict attribute for looking up length and offset info.
Open or build seqLenDict if needed'''
cls.db = db # all instances of this class are now bound to this database
from dbfile import NoSuchFileError
try: # THIS WILL FAIL IF SHELVE NOT ALREADY PRESENT...
db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','r') # READ-ONLY
except NoSuchFileError: # BUILD: READ ALL SEQ LENGTHS, STORE IN PERSIST DICT
db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','n') # NEW EMPTY FILE
logger.debug( 'building sequence indices' )
store_seqlen_dict(db.seqLenDict, filepath, **kwargs)
db.seqLenDict.close() # FORCE IT TO WRITE DATA TO DISK
db.seqLenDict = classutil.open_shelve(filepath+'.seqlen','r') # READ-ONLY
db.seqInfoDict = SeqLenDictWrapper(db) # standard interface
def __init__(self, nlmsa, filename, mode, idDictClass=None, maxSequenceCacheSize=_DEFAULT_SEQUENCE_CACHE_SIZE):
self._cache = classutil.RecentValueDictionary(maxSequenceCacheSize)
self.seqlist = NLMSASeqList(self)
self.nlmsa = nlmsa
self.filename = filename
if mode == "memory": # just use python dictionary
idDictClass = dict
elif mode == "w": # new database
mode = "n"
if idDictClass is None: # use persistent id dictionary storage
self.seqIDdict = classutil.open_shelve(filename + ".seqIDdict", mode)
self.IDdict = classutil.open_shelve(filename + ".idDict", mode)
else: # user supplied class for id dictionary storage
self.seqIDdict = idDictClass()
self.IDdict = idDictClass()
def reopen(self, mode='r'):
're-open shelve in the specified mode, and save mode on self'
self.close()
self.d = classutil.open_shelve(self.filename,
mode,
writeback=self.writeback)
self.mode = mode
def __init__(self, nlmsa, filename, mode, maxID=1000000, idDictClass=None):
dict.__init__(self)
self.seqlist = NLMSASeqList(self)
self.maxID = maxID
self.nlmsa = nlmsa
self.filename = filename
if mode == "memory": # just use python dictionary
idDictClass = dict
elif mode == "w": # new database
mode = "n"
if idDictClass is None: # use persistent id dictionary storage
self.seqIDdict = classutil.open_shelve(filename + ".seqIDdict", mode)
self.IDdict = classutil.open_shelve(filename + ".idDict", mode)
else: # user supplied class for id dictionary storage
self.seqIDdict = idDictClass()
self.IDdict = idDictClass()
def __init__(self,nlmsa,filename,mode,maxID=1000000,idDictClass=None):
dict.__init__(self)
self.seqlist=NLMSASeqList(self)
self.maxID=maxID
self.nlmsa=nlmsa
self.filename=filename
if mode=='memory': # JUST USE PYTHON DICTIONARY
idDictClass = dict
elif mode=='w': # NEW DATABASE
mode='n'
if idDictClass is None: # USE PERSISTENT ID DICTIONARY STORAGE
self.seqIDdict = classutil.open_shelve(filename+'.seqIDdict',mode)
self.IDdict = classutil.open_shelve(filename+'.idDict',mode)
else: # USER SUPPLIED CLASS FOR ID DICTIONARY STORAGE
self.seqIDdict=idDictClass()
self.IDdict=idDictClass()
def __init__(self, nlmsa, filename, mode, idDictClass=None,
maxSequenceCacheSize=_DEFAULT_SEQUENCE_CACHE_SIZE):
self._cache = classutil.RecentValueDictionary(maxSequenceCacheSize)
self.seqlist = NLMSASeqList(self)
self.nlmsa = nlmsa
self.filename = filename
if mode == 'memory': # just use python dictionary
idDictClass = dict
elif mode == 'w': # new database
mode = 'n'
if idDictClass is None: # use persistent id dictionary storage
self.seqIDdict = classutil.open_shelve(filename + '.seqIDdict',
mode)
self.IDdict = classutil.open_shelve(filename + '.idDict', mode)
else: # user supplied class for id dictionary storage
self.seqIDdict = idDictClass()
self.IDdict = idDictClass()
def _init_subclass(cls, db, filepath, **kwargs):
'''initialize our indexes if needed, and provide db with a
seqInfoDict attribute for looking up length and offset info.
Open or build seqLenDict if needed'''
cls.db = db # all instances of this class are now bound to this database
from dbfile import NoSuchFileError
try: # THIS WILL FAIL IF SHELVE NOT ALREADY PRESENT...
db.seqLenDict = classutil.open_shelve(filepath + '.seqlen',
'r') # READ-ONLY
except NoSuchFileError: # BUILD: READ ALL SEQ LENGTHS, STORE IN PERSIST DICT
db.seqLenDict = classutil.open_shelve(filepath + '.seqlen',
'n') # NEW EMPTY FILE
logger.debug('building sequence indices')
store_seqlen_dict(db.seqLenDict, filepath, **kwargs)
db.seqLenDict.close() # FORCE IT TO WRITE DATA TO DISK
db.seqLenDict = classutil.open_shelve(filepath + '.seqlen',
'r') # READ-ONLY
db.seqInfoDict = SeqLenDictWrapper(db) # standard interface
def __init__(self, filename, mode=None, writeback=False,
unpicklingMode=False, verbose=True, **kwargs):
'''Wrapper for a shelve object that can be pickled. Ideally, you
should specify a TWO letter mode string: the first letter to
indicate what mode the shelve should be initially opened in, and
the second to indicate the mode to open the shelve during unpickling.
e.g. mode='nr': to create an empty shelve (writable),
which in future will be re-opened read-only.
Also, mode=None makes it first attempt to open read-only, but if the file
does not exist will create it using mode 'c'. '''
# Mark this string as a file path.
self.filename = classutil.SourceFileName(str(filename))
self.writeback = writeback
if unpicklingMode or mode is None or mode == 'r':
# Just use mode as given.
self.mode = mode
elif mode == 'n' or mode == 'c' or mode == 'w':
# Ambiguous modes, warn & set default.
if verbose:
import sys
print >>sys.stderr, '''Warning: you opened shelve file %s
in mode '%s' but this is ambiguous for how the shelve should be
re-opened later during unpickling. By default it will be
re-opened in mode 'r' (read-only). To make it be re-opened
writable, create it in mode '%sw', or call its method
reopen('w'), which will make it be re-opened in mode 'w' now and
in later unpickling. To suppress this warning message, use the
verbose=False option.''' % (filename, mode, mode)
self.mode = 'r'
else: # PROCESS UNAMBIGUOUS TWO-LETTER mode STRING
try:
if len(mode) == 2 and mode[0] in 'ncwr' and mode[1] in 'cwr':
self.mode = mode[1] # IN FUTURE OPEN IN THIS MODE
mode = mode[0] # OPEN NOW IN THIS MODE
else:
raise ValueError('invalid mode string: ' + mode)
except TypeError:
raise ValueError('file mode must be a string!')
if unpicklingMode:
self.d = classutil.open_shelve(filename, mode, writeback,
allowReadOnly=True)
else:
self.d = classutil.open_shelve(filename, mode, writeback)
classutil.apply_itemclass(self, kwargs)
def __init__(self, filepath, reader=None, **kwargs):
# make filepath a pickleable attribute.
self.filepath = classutil.SourceFileName(str(filepath))
fullpath = self.filepath + '.seqlen'
# build the seqLenDict if it doesn't already exist
try:
seqLenDict = classutil.open_shelve(fullpath, 'r')
except NoSuchFileError:
seqLenDict = self._create_seqLenDict(fullpath, filepath, reader)
self.seqLenDict = seqLenDict
self.seqInfoDict = _SeqLenDictWrapper(self) # standard interface
# initialize base class.
dbname = os.path.basename(filepath)
SequenceDB.__init__(self, filepath=filepath, dbname=dbname, **kwargs)
def __init__(self, filepath, reader=None, **kwargs):
# make filepath a pickleable attribute.
self.filepath = classutil.SourceFileName(str(filepath))
fullpath = self.filepath + '.seqlen'
# build the seqLenDict if it doesn't already exist
try:
seqLenDict = classutil.open_shelve(fullpath, 'r')
except NoSuchFileError:
seqLenDict = self._create_seqLenDict(fullpath, filepath, reader)
self.seqLenDict = seqLenDict
self.seqInfoDict = _SeqLenDictWrapper(self) # standard interface
# initialize base class.
dbname = os.path.basename(filepath)
SequenceDB.__init__(self, filepath=filepath, dbname=dbname, **kwargs)
def reopenReadOnly(self, mode="r"):
"save existing data and reopen in read-only mode"
self.close()
self.seqIDdict = classutil.open_shelve(self.filename + ".seqIDdict", mode)
self.IDdict = classutil.open_shelve(self.filename + ".idDict", mode)
def reopenReadOnly(self, mode='r'):
'save existing data and reopen in read-only mode'
self.close()
self.seqIDdict = classutil.open_shelve(self.filename + '.seqIDdict',
mode)
self.IDdict = classutil.open_shelve(self.filename + '.idDict', mode)
def reopen(self,mode='r'):
're-open shelve in the specified mode, and save mode on self'
self.close()
self.d = classutil.open_shelve(self.filename,mode,writeback=self.writeback)
self.mode = mode
def reopenReadOnly(self,mode='r'): 'save existing data and reopen in read-only mode' self.close() self.seqIDdict = classutil.open_shelve(self.filename+'.seqIDdict',mode) self.IDdict = classutil.open_shelve(self.filename+'.idDict',mode)
