def __init__(self, f, filetype=None):
print f, filetype
self.file = getFileHandle(f, 'r')
filetype = filetype or f.split('.')[-1]
if filetype.lower() == 'm1':
self._filetype = 'm1'
self._datatype = BlasrM1
elif filetype.lower() == 'm5':
self._filetype = 'm5'
self._datatype = BlasrM5
else:
raise BlasrTypeError("Invalid type to BlasrReader")
def __init__(self, f, filetype=None):
self.file = getFileHandle(f, "r")
filetype = filetype or f.split(".")[-1]
if filetype.lower() == "m1":
self._filetype = "m1"
self._datatype = BlasrM1
elif filetype.lower() == "m4":
self._filetype = "m4"
self._datatype = BlasrM4
elif filetype.lower() == "m5":
self._filetype = "m5"
self._datatype = BlasrM5
else:
raise TypeError("Invalid type to BlasrReader")
def readFofn(f):
"""
Return iterator over filenames in a FOFN ("file-of-filenames")
file or file-like object.
If f is a path to a true FOFN on disk, any paths listed in the
FOFN that are relative (i.e., do not contain a leading '/') will
be reckoned from the directory containing the FOFN.
"""
if isinstance(f, basestring):
fofnRoot = dirname(abspath(f))
else:
fofnRoot = None
for line in getFileHandle(f):
path = line.rstrip()
if isabs(path):
yield path
elif fofnRoot is not None:
yield normpath(join(fofnRoot, path))
else:
raise IOError, "Cannot handle relative paths in StringIO FOFN"
def readFofn(f):
"""
Return iterator over filenames in a FOFN ("file-of-filenames")
file or file-like object.
If f is a path to a true FOFN on disk, any paths listed in the
FOFN that are relative (i.e., do not contain a leading '/') will
be reckoned from the directory containing the FOFN.
"""
if isinstance(f, basestring):
fofnRoot = dirname(abspath(f))
else:
fofnRoot = None
for line in getFileHandle(f):
path = line.rstrip()
if isabs(path):
yield path
elif fofnRoot is not None:
yield normpath(join(fofnRoot, path))
else:
raise IOError, "Cannot handle relative paths in StringIO FOFN"
def __init__(self, f):
self.filename = f
self.file = getFileHandle(f, "r")
def __init__(self, f):
self.file = getFileHandle(f, 'r')
def __init__(self, f):
self.file = getFileHandle(f, 'r')
def __init__(self, f):
self.filename = f
self.file = getFileHandle(f, "r")
