Access a GenBank file using a dictionary interface, though a Mindy DB.
WARNING: This is very experimental and subject to change.
It requires the use of Andrew Dalke's mindy.
This is the Dictionary interface to use after you create an index
database using the function index_file_db.
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Methods
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__getattr__
__getitem__
__init__
__len__
aliases
keys
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__getattr__
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__getattr__ ( self, name )
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__getitem__
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__getitem__ ( self, key )
Retrieve an item from the indexed file.
The key can be either a primary identifier or an alias. The lookup
will first try to get the file via the primary identifier, and if
it can't do this, will subsequently try to get it through the
aliases to these keys. If the aliases are ambigous, an error will
be raised.
Most of the time I find it easiest to search by aliases (the GenBank
accession numbers), but YMMV.
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Exceptions
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KeyError( "Multiple records found for key %s" % key )
KeyError( "No records found for key %s" % key )
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__init__
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__init__ (
self,
db_name,
db_directory,
parser=None,
)
Initialize and open up a GenBank dictionary.
Arguments:
db_name - The name of the database we should retrieve information
from. db_directory - The location of the database specified in db_name. parser - An optional argument specifying a parser object that
the records should be run through before returning the output. If
parser is None then the unprocessed contents of the file will be
returned.
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Exceptions
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SystemExit( "You must have mindy installed:\n" + "http://www.biopython.org/~dalke/mindy-0.1.tar.gz" )
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__len__
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__len__ ( self )
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aliases
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aliases ( self )
Provide all aliases in the current database.
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keys
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keys ( self )
Provide all identifiers for the current database.
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