Bio :: GenBank :: FeatureParser :: Class FeatureParser
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Class FeatureParser

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object --+

Parse GenBank files into Seq + Feature objects (OBSOLETE).

Direct use of this class is discouraged, and may be deprecated in a future release of Biopython.

Please use Bio.SeqIO.parse(...) or instead.

Instance Methods [hide private]
__init__(self, debug_level=0, use_fuzziness=1, feature_cleaner=FeatureValueCleaner())
Initialize a GenBank parser and Feature consumer.
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parse(self, handle)
Parse the specified handle.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, debug_level=0, use_fuzziness=1, feature_cleaner=FeatureValueCleaner())

source code 

Initialize a GenBank parser and Feature consumer.


  • 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.
  • use_fuzziness - Specify whether or not to use fuzzy representations. The default is 1 (use fuzziness).
  • 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.
Overrides: object.__init__