def __init__(self,
prefixDict=None,
separator='.',
filename=None,
dbClass=BlastDB,
trypath=None):
'''can either be created using prefixDict, or a header file
for a previously created PrefixUnionDict'''
if filename is not None: # READ UNION HEADER FILE
if trypath is None: # DEFAULT: LOOK IN SAME DIRECTORY AS UNION HEADER
trypath = [os.path.dirname(filename)]
ifile = file(filename)
it = iter(ifile)
separator = it.next().strip('\r\n') # DROP TRAILING CR
prefixDict = {}
for line in it:
prefix, filepath = line.strip().split('\t')[:2]
try:
prefixDict[prefix] = \
dbClass(classutil.search_dirs_for_file(filepath, trypath))
except IOError:
raise IOError(
'''unable to open database %s: check path or privileges.
Set trypath to give a list of directories to search.''' % filepath)
ifile.close()
self.separator = separator
if prefixDict is not None:
self.prefixDict = prefixDict
else:
self.prefixDict = {}
d = {}
for k, v in self.prefixDict.items():
d[v] = k # CREATE A REVERSE MAPPING
self.dicts = d
self.seqInfoDict = PUDSeqInfoDict(self) # standard interface
def __init__(self,prefixDict=None,separator='.',filename=None,
dbClass=BlastDB,trypath=None):
'''can either be created using prefixDict, or a header file
for a previously created PrefixUnionDict'''
if filename is not None: # READ UNION HEADER FILE
if trypath is None: # DEFAULT: LOOK IN SAME DIRECTORY AS UNION HEADER
trypath=[os.path.dirname(filename)]
ifile=file(filename)
it=iter(ifile)
separator=it.next().strip('\r\n') # DROP TRAILING CR
prefixDict={}
for line in it:
prefix,filepath=line.strip().split('\t')[:2]
try:
prefixDict[prefix] = \
dbClass(classutil.search_dirs_for_file(filepath, trypath))
except IOError:
raise IOError('''unable to open database %s: check path or privileges.
Set trypath to give a list of directories to search.'''
% filepath)
ifile.close()
self.separator=separator
if prefixDict is not None:
self.prefixDict=prefixDict
else:
self.prefixDict={}
d={}
for k,v in self.prefixDict.items():
d[v]=k # CREATE A REVERSE MAPPING
self.dicts=d
self.seqInfoDict = PUDSeqInfoDict(self) # standard interface
def __init__(self,
prefixDict=None,
separator='.',
filename=None,
dbClass=SequenceFileDB,
trypath=None):
# read union header file
if filename is not None:
if prefixDict:
raise TypeError('''
cannot create with prefixDict and filename both!''')
if trypath is None:
trypath = [os.path.dirname(filename)]
ifile = file(filename, 'rU')
try:
it = iter(ifile)
# Remove leading/trailing CR+LF.
separator = it.next().strip('\r\n')
prefixDict = {}
for line in it:
prefix, filepath = line.strip().split('\t')[:2]
try:
dbfile = classutil.search_dirs_for_file(
filepath, trypath)
db = dbClass(dbfile)
except IOError:
for db in prefixDict.values():
db.close() # close databases before exiting
raise IOError('''\
unable to open database %s: check path or privileges.
Set 'trypath' to give a list of directories to search.''' % filepath)
else:
prefixDict[prefix] = db
finally:
ifile.close()
self.separator = separator
if prefixDict is not None:
self.prefixDict = prefixDict
else:
self.prefixDict = {}
# also create a reverse mapping
d = {}
for k, v in self.prefixDict.items():
d[v] = k
self.dicts = d
self.seqInfoDict = _PUDSeqInfoDict(self) # supply standard interface
def __init__(self, prefixDict=None, separator=".", filename=None, dbClass=SequenceFileDB, trypath=None):
# read union header file
if filename is not None:
if prefixDict:
raise TypeError(
"""
cannot create with prefixDict and filename both!"""
)
if trypath is None:
trypath = [os.path.dirname(filename)]
ifile = file(filename, "rU")
try:
it = iter(ifile)
separator = it.next().strip("\r\n") # remove leading/trailing CR
prefixDict = {}
for line in it:
prefix, filepath = line.strip().split("\t")[:2]
try:
dbfile = classutil.search_dirs_for_file(filepath, trypath)
db = dbClass(dbfile)
except IOError:
for db in prefixDict.values():
db.close() # close databases before exiting
raise IOError(
"""\
unable to open database %s: check path or privileges.
Set 'trypath' to give a list of directories to search."""
% filepath
)
else:
prefixDict[prefix] = db
finally:
ifile.close()
self.separator = separator
if prefixDict is not None:
self.prefixDict = prefixDict
else:
self.prefixDict = {}
# also create a reverse mapping
d = {}
for k, v in self.prefixDict.items():
d[v] = k
self.dicts = d
self.seqInfoDict = _PUDSeqInfoDict(self) # supply standard interface
