def __init__(self, filename, format):
"""Initialize the class."""
self._handle = _open_for_random_access(filename)
self._format = format
# Load the parser class/function once an avoid the dict lookup in each
# __getitem__ call:
self._iterator = SeqIO._FormatToIterator[format]
def __init__(self, filename, format, alphabet):
"""Initialize the class."""
self._handle = _open_for_random_access(filename)
self._alphabet = alphabet
self._format = format
# Load the parser class/function once an avoid the dict lookup in each
# __getitem__ call:
i = SeqIO._FormatToIterator[format]
# The following alphabet code is a bit nasty... duplicates logic in
# Bio.SeqIO.parse()
if alphabet is None:
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
return next(i(handle))
else:
# TODO - Detect alphabet support ONCE at __init__
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
try:
return next(i(handle, alphabet=alphabet))
except TypeError:
return next(SeqIO._force_alphabet(i(handle), alphabet))
self._parse = _parse
def __init__(self, filename, format, alphabet):
self._handle = _open_for_random_access(filename)
self._alphabet = alphabet
self._format = format
#Load the parser class/function once an avoid the dict lookup in each
#__getitem__ call:
i = SeqIO._FormatToIterator[format]
#The following alphabet code is a bit nasty... duplicates logic in
#Bio.SeqIO.parse()
if alphabet is None:
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
return next(i(handle))
else:
#TODO - Detect alphabet support ONCE at __init__
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
try:
return next(i(handle, alphabet=alphabet))
except TypeError:
return next(SeqIO._force_alphabet(i(handle), alphabet))
self._parse = _parse
def __init__(self, filename, **kwargs):
self._handle = _open_for_random_access(filename)
self._kwargs = kwargs
def __init__(self, filename, **kwargs):
"""Initialize the class."""
self._handle = _open_for_random_access(filename)
self._kwargs = kwargs
