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Deprecating Bio.SeqUtils.makeTableX function, plus ProteinX and Missi…

…ngTable classes which are all dead code after the removal of the Bio.SeqUtils.translate function
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1 parent 0d6a55c commit 8135f463012e5056614ebfd16082a3a1f89cd795 @peterjc peterjc committed Feb 4, 2010
Showing with 9 additions and 0 deletions.
  1. +5 −0 Bio/SeqUtils/__init__.py
  2. +4 −0 DEPRECATED
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5 Bio/SeqUtils/__init__.py
@@ -221,13 +221,18 @@ def nt_search(seq, subseq):
# should be moved to ???
class ProteinX(Alphabet.ProteinAlphabet):
+ """Variant of the extended IUPAC extended protein alphabet (DEPRECATED)."""
letters = IUPACData.extended_protein_letters + "X"
+#Can't add a deprecation warning to the class due to the following line:
proteinX = ProteinX()
class MissingTable:
def __init__(self, table):
self._table = table
+ import warnings
+ warnings.warn("Function Bio.SeqUtils.makeTableX() and related classes ProteinX "
+ "and MissingTable are deprecated.", DeprecationWarning)
def get(self, codon, stop_symbol):
try:
return self._table.get(codon, stop_symbol)
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4 DEPRECATED
@@ -309,6 +309,10 @@ 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.
+Function makeTableX and classes ProteinX and MissingTable were deprecated
+in Release 1.54. These were remnants of the removed translate function,
+and no longer served any useful purpose.
+
Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, instead
just use the string's slice method with a step of minus one.

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