From 74fe3dd40c6f1f43032fa490a918abf052fd5c0e Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 15 Jul 2013 14:01:13 +0100 Subject: [PATCH] Deprecated Bio.Motif as discussed on the mailing list --- Bio/Motif/__init__.py | 22 +++++++++++----------- DEPRECATED | 5 +++++ 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/Bio/Motif/__init__.py b/Bio/Motif/__init__.py index 02f0157901e..4ca72df8614 100644 --- a/Bio/Motif/__init__.py +++ b/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 diff --git a/DEPRECATED b/DEPRECATED index 87be4c87ac9..2063c2d654f 100644 --- a/DEPRECATED +++ b/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