Bio.GenBank._BaseGenBankConsumer

Class _BaseGenBankConsumer

object --+ | _BaseGenBankConsumer

Abstract GenBank consumer providing useful general functions (PRIVATE). This just helps to eliminate some duplication in things that most GenBank consumers want to do.

Instance Methods

[hide private]

__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

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_unhandled(self, data)

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__getattr__(self, attr)

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_split_keywords(self, keyword_string)
Split a string of keywords into a nice clean list.

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_split_accessions(self, accession_string)
Split a string of accession numbers into a list.

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_split_taxonomy(self, taxonomy_string)
Split a string with taxonomy info into a list.

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_clean_location(self, location_string)
Clean whitespace out of a location string.

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_remove_newlines(self, text)
Remove any newlines in the passed text, returning the new string.

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_normalize_spaces(self, text)
Replace multiple spaces in the passed text with single spaces.

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_remove_spaces(self, text)
Remove all spaces from the passed text.

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_convert_to_python_numbers(self, start, end)
Convert a start and end range to python notation.

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables

[hide private]

remove_space_keys = ['translation']

Properties

[hide private]

Inherited from object: __class__

init(self)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

_clean_location(self, location_string)

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Clean whitespace out of a location string.

The location parser isn't a fan of whitespace, so we clean it out
before feeding it into the parser.

_convert_to_python_numbers(self, start, end)

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Convert a start and end range to python notation.

In GenBank, starts and ends are defined in "biological" coordinates,
where 1 is the first base and [i, j] means to include both i and j.

In python, 0 is the first base and [i, j] means to include i, but
not j.

So, to convert "biological" to python coordinates, we need to
subtract 1 from the start, and leave the end and things should
be converted happily.

Class _BaseGenBankConsumer

__init__(self) (Constructor)

_clean_location(self, location_string)

_convert_to_python_numbers(self, start, end)

init(self)
(Constructor)