def __init__(self,
iFileHandle,
clobber=False,
interface=Interface.CONTAINER,
method=IndexMethod.SQLITE,
**kw):
"""Constructor
@param iFileHandle: Name of input file
"""
self.iFile = smartopen(iFileHandle)
self.iFilename = self.iFile.name
if method == IndexMethod.PICKLE:
self.indexFile = fasta.FastaIndexPickleFile(self.iFilename)
elif method == IndexMethod.TEXT:
self.indexFile = fasta.FastaIndexTextFile(self.iFilename)
else: # sqlite3 method is the default
self.indexFile = fasta.FastaIndexFile(self.iFilename)
self.indexFile.build(clobber=clobber)
self.interface = interface
self._iter = None
self._initIter = True
if kw:
print 'Uncaptured keywords'
print kw
def __init__(self, fileHandle, header=None, separator="\t", mode='w', **kw):
"""
@param iFileHandle: Output file or name
@keyword mode: File mode - write(w) or append(a)
"""
assert mode in ('w', 'a')
self.iFile = smartopen(fileHandle, mode)
self.iFilename = self.iFile.name
self.separator = separator
if header:
self.iFile.write(header + "\n")
def __init__(self, iFileHandle, header=False, separator="\t"):
"""
Constructor
@param iFileHandle: File name or object
@keyword header: Skip header line (default False)
@keyword separator: Column separator/delimiter (default '\\t')
"""
self.iFile = smartopen(iFileHandle)
self.separator = separator
if header:
headerline = self.iFile.readline()
def __init__(self, iFileHandle, header=False, separator="\t"):
"""
Constructor
@param iFileHandle: File name or object
@keyword header: Skip header line (default False)
@keyword separator: Column separator/delimiter (default '\\t')
"""
self.iFile = smartopen(iFileHandle)
self.separator = separator
if header:
headerline = self.iFile.readline()
def __init__(self,
fileHandle,
header=None,
separator="\t",
mode='w',
**kw):
"""
@param iFileHandle: Output file or name
@keyword mode: File mode - write(w) or append(a)
"""
assert mode in ('w', 'a')
self.iFile = smartopen(fileHandle, mode)
self.iFilename = self.iFile.name
self.separator = separator
if header:
self.iFile.write(header + "\n")
def __init__(self, iFileHandle, mode='w', width=60, blockSize=None, **kw):
"""
@param iFileHandle: Output file or name
@keyword mode: File mode - write(w) or append(a)
"""
assert mode in ('w', 'a')
self.iFile = smartopen(iFileHandle, mode)
self.iFilename = self.iFile.name
self.width = width
if blockSize:
self.setBlockSize(blockSize)
if kw:
print 'Uncaptured keywords'
print kw
def __init__(self, iFileHandle, mode='w', width=60, blockSize=None, **kw):
"""
@param iFileHandle: Output file or name
@keyword mode: File mode - write(w) or append(a)
"""
assert mode in ('w', 'a')
self.iFile = smartopen(iFileHandle, mode)
self.iFilename = self.iFile.name
self.width = width
if blockSize:
self.setBlockSize(blockSize)
if kw:
print 'Uncaptured keywords'
print kw
def __init__(self,
iFileHandle,
columns,
converters=None,
header=True,
separator='\t',
**kw):
"""
Constructor
@param iFileHandle: File name or object
@keyword columns: List of column names (default None)
@keyword converters: List of types or conversion functions (default None)
@keyword header: Skip header line (default True)
@keyword separator: Column separator/delimiter (default '\\t')
"""
self.iFile = smartopen(iFileHandle)
self.columns = columns
if converters == None:
converters = []
for name in columns:
if "start" in name or "end" in name:
converters.append(int)
elif "strand" in name:
converters.append(strandConverter)
else:
converters.append(None)
elif type(converters) == list and type(
converters[0]) == tuple: # list of tuples
converters = dict(converters)
converters = [converters.get(column) for column in columns]
self.converters = converters
self.separator = separator
if header:
headerline = self.iFile.readline()
if 'fields' in kw:
warnings.warn("Deprecated keyword fields. Use columns",
category=DeprecationWarning)
self.columns = kw['fields']
if 'sep' in kw:
warnings.warn("Deprecated keyword fields. Use columns",
category=DeprecationWarning)
self.separator = kw['sep']
def __init__(self, iFileHandle, columns, converters=None, header=True, separator='\t', **kw):
"""
Constructor
@param iFileHandle: File name or object
@keyword columns: List of column names (default None)
@keyword converters: List of types or conversion functions (default None)
@keyword header: Skip header line (default True)
@keyword separator: Column separator/delimiter (default '\\t')
"""
self.iFile = smartopen(iFileHandle)
self.columns = columns
if converters==None:
converters = []
for name in columns:
if "start" in name or "end" in name:
converters.append(int)
elif "strand" in name:
converters.append(strandConverter)
else:
converters.append(None)
elif type(converters)==list and type(converters[0])==tuple: # list of tuples
converters = dict(converters)
converters = [converters.get(column) for column in columns]
self.converters = converters
self.separator = separator
if header:
headerline = self.iFile.readline()
if 'fields' in kw:
warnings.warn("Deprecated keyword fields. Use columns",
category=DeprecationWarning)
self.columns = kw['fields']
if 'sep' in kw:
warnings.warn("Deprecated keyword fields. Use columns",
category=DeprecationWarning)
self.separator = kw['sep']
def __init__(self, iFileHandle, clobber=False,
interface=Interface.CONTAINER, method=IndexMethod.SQLITE, **kw):
"""
@param iFileHandle: Fasta file name or object
"""
self.iFile = smartopen(iFileHandle)
self.iFilename = self.iFile.name
if method==IndexMethod.PICKLE:
self.indexFile = FastaIndexPickleFile(self.iFilename)
elif method==IndexMethod.TEXT:
self.indexFile = FastaIndexTextFile(self.iFilename)
else: # sqlite3 method is the default
self.indexFile = FastaIndexFile(self.iFilename)
self.indexFile.build(clobber=clobber)
self.interface = interface
self._iter = None
self._initIter = True
if kw:
print 'Uncaptured keywords'
print kw
def __init__(self, iFileHandle):
self.iFile = smartopen(iFileHandle)
self.iFilename = self.iFile.name
self._iter = None