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Remove deprecated Bio.Restriction.DNAUtils and check_bases

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commit e0e37e1d59ba4838541c6ede0edf73f8c76f3e9a 1 parent 279d220
Peter Cock peterjc authored
28 Bio/Restriction/DNAUtils.py
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@@ -1,28 +0,0 @@
-# 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.
-
-"""DNA utilities for Bio.Restriction (DEPRECATED).
-
-DNAUtils was written in C and therefore would not be available on Jython etc.
-It offered three string based functions:
- - complement, duplicating the functionality of the Seq object
- - antiparallel, duplicating the functionality of the Seq object and
- the reverse_complement function in Bio.Seq
- - check_bases, a very odd validation routine unlikely to be of general use.
-"""
-
-import warnings
-warnings.warn("Bio.Restriction.DNAUtils is deprecated, and will be "
- "removed in a future release of Biopython.")
-del warnings
-
-#expose these existing functions mimicking the old DNAUtils names:
-from Bio.Seq import reverse_complement as antiparallel
-
-#quick and dirty complement function, maybe we should add one to Bio.Seq?
-def complement(seq_string) :
- return antiparallel(seq_string)[::-1]
-
-#expose this re-implementation of the old C code function check_bases:
-from Bio.Restriction.Restriction import _check_bases as check_bases
7 Bio/Restriction/Restriction.py
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@@ -113,13 +113,6 @@ def _check_bases(seq_string):
raise TypeError("Invalid character found in %s" % repr(seq_string))
return " " + seq_string
-def check_bases(seq_string):
- """Check characters in a string (DEPRECATED)."""
- import warnings
- import Bio
- warnings.warn("The check_bases function has been deprecated, and will be"
- "removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
- return _check_bases(seq_string)
matching = {'A' : 'ARWMHVDN', 'C' : 'CYSMHBVN', 'G' : 'GRSKBVDN',
'T' : 'TYWKHBDN', 'R' : 'ABDGHKMNSRWV', 'Y' : 'CBDHKMNSTWVY',
2  DEPRECATED
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@@ -46,7 +46,7 @@ Bio.Restriction.DNAUtils and check_bases
This module (originally in C) offered complement and antiparallel functions
(duplicating functionality in Bio.Seq) and a rather odd function called
check_bases (also available as Bio.Restriction.Restriction.check_bases).
-Deprecated in Release 1.53.
+Deprecated in Release 1.53, removed in Release 1.57.
Bio.Blast.NCBIStandalone
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