Package Bio :: Package GFF
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Package GFF

source code

Access to General Feature Format databases created with Bio::DB:GFF

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 $

Submodules [hide private]

Classes [hide private]
  Segment
this will only work for the simplest of easy.Location objects
  Connection
Connection to GFF database
  RetrieveSeqname
Singleton: contain records of loaded FASTA files
  Feature
strand may be: +/0 = Watson -/1 = Crick
  FeatureQueryRow
row of FeatureQuery results works like a Feature
  FeatureQuery
SELECT fdata.fref AS seqname,...
  FeatureAggregate
Functions [hide private]
 
object2fgroup_sql(object) source code
 
object_split(object) source code
 
_test(*args, **keywds) source code
Variables [hide private]
  DEFAULT_ALPHABET = IUPACUnambiguousDNA()