Package Bio :: Package GFF

Package GFF

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 $

Submodules

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Bio.GFF.GenericTools: A set of generic bits of code under Bio.GFF (DEPRECATED).
Bio.GFF.binning: Binning support for Bio.GFF (DEPRECATED)
Bio.GFF.easy: Bio.GFF.easy: some functions to ease the use of Biopython (DEPRECATED)

Classes

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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...

FeatureQuery
SELECT fdata.fref AS seqname,...

FeatureAggregate
>>> feature1_1 = Feature(location=easy.LocationFromString("NC_001802x.fna:336..1631"), frame=0) # gag-pol >>> feature1_2 = Feature(location=easy.LocationFromString("NC_001802x.fna:1631..4642"), frame=0) # slippage >>> aggregate = FeatureAggregate([feature1_1, feature1_2]) >>> print aggregate.location() join(NC_001802x.fna:336..1631,NC_001802x.fna:1631..4642) >>> xlate_str = aggregate.translate().tostring() >>> xlate_str[:5], xlate_str[-5:] ('MGARA', 'RQDED')

Functions

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object2fgroup_sql(object)

source code

object_split(object)
>>> object_split("Sequence:F02E9.2a")...

source code

_test(*args, **keywds)

source code

Variables

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DEFAULT_ALPHABET = IUPACUnambiguousDNA()

__warningregistry__ = {('The old Bio.GFF module for access to ...

Function Details

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object_split(object)

source code


>>> object_split("Sequence:F02E9.2a")
('Sequence', 'F02E9.2a')

Variables Details

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warningregistry

Value:

{('The old Bio.GFF module for access to a MySQL GFF database created w
ith BioPerl is deprecated, and will be removed (or possibly just moved
) in a future release of Biopython.  If you want to continue to use th
is code, please get in contact with the developers via the mailing lis
ts to avoid its permanent removal from Biopython. The plan is to re-us
e the Bio.GFF namespace for a new GFF parsing module.',
  <class 'Bio.BiopythonDeprecationWarning'>,
  34): 1}