class FeatureParser:
"""Parse GenBank files into Seq + Feature objects.
"""
def __init__(self, debug_level = 0, use_fuzziness = 1,
feature_cleaner = FeatureValueCleaner()):
"""Initialize a GenBank parser and Feature consumer.
Arguments:
o debug_level - An optional argument that species the amount of
debugging information the parser should spit out. By default we have
no debugging info (the fastest way to do things), but if you want
you can set this as high as two and see exactly where a parse fails.
o use_fuzziness - Specify whether or not to use fuzzy representations.
The default is 1 (use fuzziness).
o feature_cleaner - A class which will be used to clean out the
values of features. This class must implement the function
clean_value. GenBank.utils has a "standard" cleaner class, which
is used by default.
"""
self._scanner = GenBankScanner(debug_level)
self.use_fuzziness = use_fuzziness
self._cleaner = feature_cleaner
def parse(self, handle):
"""Parse the specified handle.
"""
self._consumer = _FeatureConsumer(self.use_fuzziness,
self._cleaner)
self._scanner.feed(handle, self._consumer)
return self._consumer.data
def __init__(self, debug_level = 0):
"""Initialize the parser.
Arguments:
o debug_level - An optional argument that species the amount of
debugging information the parser should spit out. By default we have
no debugging info (the fastest way to do things), but if you want
you can set this as high as two and see exactly where a parse fails.
"""
self._scanner = GenBankScanner(debug_level)
class RecordParser:
"""Parse GenBank files into Record objects
"""
def __init__(self, debug_level = 0):
"""Initialize the parser.
Arguments:
o debug_level - An optional argument that species the amount of
debugging information the parser should spit out. By default we have
no debugging info (the fastest way to do things), but if you want
you can set this as high as two and see exactly where a parse fails.
"""
self._scanner = GenBankScanner(debug_level)
def parse(self, handle):
"""Parse the specified handle into a GenBank record.
"""
self._consumer = _RecordConsumer()
self._scanner.feed(handle, self._consumer)
return self._consumer.data
