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Deprecating Bio.GFF as discussed on the mailing list

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commit dc5c326a520c9ff67ead19f83d127b7540b3f9db 1 parent 3e3e15f
@peterjc peterjc authored
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11 Bio/GFF/GenericTools.py
@@ -5,12 +5,13 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""
-A set of generic bits of code under Bio.GFF (possibly obsolete).
-"""
+"""A set of generic bits of code under Bio.GFF (DEPRECATED).
-__version__ = "$Revision: 1.6 $"
-# $Source: /home/bartek/cvs2bzr/biopython_fastimport/cvs_repo/biopython/Bio/GFF/GenericTools.py,v $
+This is part of the "old" Bio.GFF module by Michael Hoffman, which offered
+access to a MySQL database holding GFF data loaded by BioPerl. This code has
+now been deprecated, and will probably be removed in order to free the Bio.GFF
+namespace for a new GFF parser in Biopython (including GFF3 support).
+"""
import exceptions
import os
View
19 Bio/GFF/__init__.py
@@ -5,10 +5,14 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""
-Access to General Feature Format databases created with Bio::DB: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
+Based on documentation for Lincoln Stein's Perl Bio::DB::GFF
>>> import os
>>> import Bio.GFF
@@ -19,6 +23,15 @@
"""
+import warnings
+warnings.warn("The old Bio.GFF module for access to a MySQL GFF database "
+ "created with BioPerl is deprecated, and will be removed (or "
+ "possibly just moved) in a future release of Biopython. If you "
+ "want to continue to use this code, please get in contact with "
+ "the developers via the mailing lists to avoid its permanent "
+ "removal from Biopython. The plan is to re-use the Bio.GFF "
+ "namespace for a new GFF parsing module.", DeprecationWarning)
+
__version__ = "$Revision: 1.10 $"
# $Source: /home/bartek/cvs2bzr/biopython_fastimport/cvs_repo/biopython/Bio/GFF/__init__.py,v $
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11 Bio/GFF/binning.py
@@ -8,12 +8,13 @@
# note:
# I used Lincoln Stein's perl Bio::DB::GFF::Util::Binning as a model for this
-"""
-Binning support for Bio.GFF
-"""
+"""Binning support for Bio.GFF (DEPRECATED)
-__version__ = "$Revision: 1.1 $"
-# $Source: /home/bartek/cvs2bzr/biopython_fastimport/cvs_repo/biopython/Bio/GFF/binning.py,v $
+This is part of the "old" Bio.GFF module by Michael Hoffman, which offered
+access to a MySQL database holding GFF data loaded by BioPerl. This code has
+now been deprecated, and will probably be removed in order to free the Bio.GFF
+namespace for a new GFF parser in Biopython (including GFF3 support).
+"""
class Meta(object):
MIN_BIN = 1000
View
14 Bio/GFF/easy.py
@@ -5,12 +5,16 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""
-Bio.GFF.easy: some functions to ease the use of Biopython
-"""
+"""Bio.GFF.easy: some functions to ease the use of Biopython (DEPRECATED)
-__version__ = "$Revision: 1.12 $"
-# $Source: /home/bartek/cvs2bzr/biopython_fastimport/cvs_repo/biopython/Bio/GFF/easy.py,v $
+This is part of the "old" Bio.GFF module by Michael Hoffman, which offered
+access to a MySQL database holding GFF data loaded by BioPerl. This code has
+now been deprecated, and will probably be removed in order to free the Bio.GFF
+namespace for a new GFF parser in Biopython (including GFF3 support).
+
+Some of the more useful ideas of Bio.GFF.easy may be reworked for Bio.GenBank,
+using the standard SeqFeature objects used elsewhere in Biopython.
+"""
import copy
import re
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5 DEPRECATED
@@ -301,12 +301,15 @@ in Release 1.31, and removed in Release 1.43. Function 'translate' was
deprecated in Release 1.49, and removed in Release 1.53. Use the functions
and methods in Bio.Seq instead.
-Bio.GFF
+Bio.GFF (for accessing a MySQL database created with BioPerl, etc)
=======
The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
been deprecated as of Release 1.31, and removed in Release 1.43.
Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
+The whole of the old Bio.GFF module was deprecated in Release 1.53
+(with the intention of reusing this name space for a GFF parser).
+
Bio.sequtils
============
Deprecated as of Release 1.30, removed in Release 1.42.
View
2  Tests/run_tests.py
@@ -40,8 +40,6 @@
"Bio.Blast.Applications",
"Bio.Clustalw",
"Bio.Emboss.Applications",
- "Bio.GFF.easy",
- "Bio.GFF.GenericTools",
"Bio.KEGG.Compound",
"Bio.KEGG.Enzyme",
"Bio.Wise",
View
17 Tests/test_GFF.py
@@ -9,21 +9,10 @@
if not os.environ.has_key("MYSQLPASS"):
raise MissingExternalDependencyError("Environment is not configured for this test (not important if you do not plan to use Bio.GFF).")
+import warnings
+warnings.filterwarnings("ignore", category=DeprecationWarning)
import Bio.GFF
-
-"""
-#Moved these tests to test_GFF2.py as they don't need the SQL database
-import Bio.GFF.GenericTools
-import Bio.GFF.easy
-
-print "Running Bio.GFF.GenericTools doctests..."
-Bio.GFF.GenericTools._test()
-print "Bio.GFF.GenericTools doctests complete."
-
-print "Running Bio.GFF.easy doctests..."
-Bio.GFF.easy._test()
-print "Bio.GFF.easy doctests complete."
-"""
+warnings.resetwarnings()
print "Running Bio.GFF doctests..."
Bio.GFF._test()
View
4 Tests/test_GFF2.py
@@ -1,9 +1,13 @@
#!/usr/bin/env python
"""Test the Bio.GFF dependencies
"""
+
+import warnings
+warnings.filterwarnings("ignore", category=DeprecationWarning)
import Bio.GFF
import Bio.GFF.GenericTools
import Bio.GFF.easy
+warnings.resetwarnings()
print "Running Bio.GFF.GenericTools doctests..."
Bio.GFF.GenericTools._test()
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