Package GFF
source code
Access to General Feature Format databases created with BioPerl
(DEPRECATED).
This is the "old" Bio.GFF module by Michael Hoffman, which
offers access to a MySQL database holding GFF data loaded by BioPerl.
This code has now been deprecated, and will be removed (or at best,
relocated) in order to free the Bio.GFF namespace for a new GFF parser in
Biopython (including GFF3 support).
Based on documentation for Lincoln Stein's Perl Bio::DB::GFF
>>> import os
>>> import Bio.GFF
>>> PASSWORD = os.environ['MYSQLPASS']
>>> DATABASE_GFF = 'wormbase_ws93'
>>> FASTADIR = '/local/wormbase_ws93/'
>>> gff = Bio.GFF.Connection(passwd=PASSWORD, db=DATABASE_GFF, fastadir=FASTADIR)
Version:
$Revision: 1.10 $
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DEFAULT_ALPHABET = IUPACUnambiguousDNA()
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