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Deprecated Bio.Motif as discussed on the mailing list

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commit 74fe3dd40c6f1f43032fa490a918abf052fd5c0e 1 parent 45c28fa
@peterjc peterjc authored
Showing with 16 additions and 11 deletions.
  1. +11 −11 Bio/Motif/__init__.py
  2. +5 −0 DEPRECATED
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22 Bio/Motif/__init__.py
@@ -2,11 +2,11 @@
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""Tools for sequence motif analysis (OBSOLETE, see Bio.motifs instead).
+"""Tools for sequence motif analysis (DEPRECATED, see Bio.motifs instead).
-This module (Bio.Motif) is now obsolete, and will be deprecated and
-removed in a future release of release of Biopython. Please use the
-new module Bio.motifs instead.
+This module (Bio.Motif) has been deprecated and will be removed in a
+future release of release of Biopython. Please use the new module
+Bio.motifs instead.
This contains the core Motif class containing various I/O methods as
well as methods for motif comparisons and motif searching in sequences.
@@ -14,14 +14,14 @@
"""
import warnings
-warnings.warn("The module Bio.Motif is now obsolete, and will be"
- "deprecated and removed in a future release of"
- "release of Biopython. As a replacement for Bio.Motif,"
- "please use the new module Bio.motifs instead. Please"
- "be aware that though the functionality of Bio.Motif"
- "is retained (and extended) in Bio.motifs, usage may"
+from Bio import BiopythonDeprecationWarning
+warnings.warn("The module Bio.Motif has been depreacted and will be "
+ "removed in a future release of Biopython. Instead "
+ "please use the new module Bio.motifs instead. Please "
+ "be aware that though the functionality of Bio.Motif "
+ "is retained (and extended) in Bio.motifs, usage may "
"be different.",
- PendingDeprecationWarning)
+ BiopythonDeprecationWarning)
from Bio.Motif._Motif import Motif
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5 DEPRECATED
@@ -33,6 +33,11 @@ Bio.SeqFeature
With the introduction of the CompoundLocation in Release 1.62, the SeqFeature
attribute sub_features was deprecated.
+Bio.Motif
+=========
+Declared obsolete with a PendingDeprecationWarning in Release 1.61, formerly
+deprecated in Release 1.62. Please use the newer Bio.motifs module instead.
+
AlignAceCommandline and CompareAceCommandline
=============================================
Deprecated in release 1.62. An up to date version of the software cannot
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