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Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …

…be deprecated in a future release.
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1 parent 79e6dfc commit 41a4497403a0f72a3860cf51f7f117df60b0d683 @peterjc peterjc committed Oct 28, 2008
Showing with 22 additions and 14 deletions.
  1. +6 −1 Bio/Transcribe.py
  2. +8 −9 Bio/Translate.py
  3. +8 −4 DEPRECATED
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@@ -1,6 +1,11 @@
"""Code to transcribe DNA into RNA or back (OBSOLETE).
-You are now encouraged to use the functions in Bio.Seq instead."""
+You are now encouraged to use the Seq object methods or the functions
+in Bio.Seq instead.
+
+This module is now considered to be obsolete, and is likely to be deprecated
+in a future release of Biopython, and later removed.
+"""
import string
from Bio import Alphabet, Seq
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@@ -1,17 +1,16 @@
-"""Code to translate DNA or RNA into proteins (semi-obsolete).
+"""Code to translate DNA or RNA into proteins (OBSOLETE).
Instead of Bio.Translate, for translation you are now encouraged to use the
Seq object's translate method, or the translate function in the Bio.Seq
-module.
+module. Translate-to-stop functionality is via an optional argument.
-However, at the time of writing, Bio.Seq does not yet offer the full
-functionality of Bio.Translate, lacking in particular back-translation and
-translate-to-stop.
+Bio.Seq does not offer any back-translation function like the one here. It
+was concluded that a since a simple back-translation giving a Seq or python
+string could only capture some of the possible back translations, there were
+no practical uses for such a method/function.
-The provisional intension is to add back-translation and translate-to-stop
-functionality to Bio.Seq, and then declare Bio.Translate as obsolete. This
-module would then be deprecated, and later removed in a future release of
-Biopython.
+This module is now considered to be obsolete, and is likely to be deprecated
+in a future release of Biopython, and later removed.
"""
from Bio import Alphabet, Seq
from Bio.Data import CodonTable
View
@@ -4,14 +4,20 @@ to find documentation about how to update your code to work again.
Numeric support
===============
-Following the release of 1.48, Numeric support in Biopython is discontinued. Please move to NumPy.
+Following the release of 1.48, Numeric support in Biopython is discontinued.
+Please move to NumPy.
Bio.Seq
=======
Direct use of the Seq object (and MutableSeq object) .data property is discouraged.
As of release 1.49, writing to the Seq object's .data property triggers a warning,
and this property is likely to be made read only in the next release.
+Bio.Transcribe and Bio.Translate
+================================
+Declared obsolete in Release 1.49.
+Please use the methods or functions in Bio.Seq instead.
+
Martel
======
Declared obsolete in Release 1.48, deprecated in Release 1.49.
@@ -183,9 +189,7 @@ Bio.RecordFile
==============
Deprecated as of Release 1.30, removed in Release 1.42.
RecordFile wasn't completely implemented and duplicates the work
-of most standard parsers. We recommend using a specific iterator
-(Bio.Fasta.Iterator for example) without a parser to get back
-text records.
+of most standard parsers.
Bio.kMeans and Bio.xkMeans
==========================

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