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removed the deprecated functions translate, translate_to_stop, back_t…

…ranslate, transcribe, and back_transcribe from Bio.utils
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1 parent c88763f commit 999d2e44df795db25703510e4f8aa03f931095ba mdehoon committed
Showing with 6 additions and 67 deletions.
  1. +0 −67 Bio/utils.py
  2. +6 −0 DEPRECATED
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67 Bio/utils.py
@@ -11,73 +11,6 @@
from PropertyManager import default_manager
-def translate(seq, id = None):
- """Translate a sequence (DEPRECATED)."""
- import warnings
- warnings.warn("Bio.utils.translate() has been deprecated, and we"
- " intend to remove it in a future release of Biopython."
- " Please use the translate method or function in Bio.Seq"
- " instead, as described in the Tutorial.",
- DeprecationWarning)
- if id is None:
- s = "translator"
- else:
- s = "translator.id.%d" % id
- translator = default_manager.resolve(seq.alphabet, s)
- return translator.translate(seq)
-
-def translate_to_stop(seq, id = None):
- """Translate a sequence up to the first in frame stop codon (DEPRECATED)."""
- import warnings
- warnings.warn("Bio.utils.translate_to_stop() has been deprecated, and we"
- " intend to remove it in a future release of Biopython."
- " Please use the translate method or function in Bio.Seq"
- " instead, as described in the Tutorial.",
- DeprecationWarning)
- if id is None:
- s = "translator"
- else:
- s = "translator.id.%d" % id
- translator = default_manager.resolve(seq.alphabet, s)
- return translator.translate_to_stop(seq)
-
-def back_translate(seq, id = None):
- """Back-translate a sequence (DEPRECATED)."""
- import warnings
- warnings.warn("Bio.utils.back_translate() has been deprecated, and we"
- " intend to remove it in a future release of Biopython."
- " If you use it, please tell us on the mailing list.",
- DeprecationWarning)
- if id is None:
- s = "translator"
- else:
- s = "translator.id.%d" % id
- translator = default_manager.resolve(seq.alphabet, s)
- return translator.back_translate(seq)
-
-
-def transcribe(seq):
- """Transcribe a sequence (DEPRECATED)."""
- import warnings
- warnings.warn("Bio.utils.transcribe() has been deprecated, and we"
- " intend to remove it in a future release of Biopython."
- " Please use the transcribe method or function in"
- " Bio.Seq instead, as described in the Tutorial.",
- DeprecationWarning)
- transcriber = default_manager.resolve(seq.alphabet, "transcriber")
- return transcriber.transcribe(seq)
-
-def back_transcribe(seq):
- """Back-transcribe a sequence (DEPRECATED)."""
- import warnings
- warnings.warn("Bio.utils.back_transcribe() has been deprecated, and we" \
- " intend to remove it in a future release of Biopython."\
- " Please use the back_transcribe method or function in"\
- " Bio.Seq instead, as described in the Tutorial.",
- DeprecationWarning)
- transcriber = default_manager.resolve(seq.alphabet, "transcriber")
- return transcriber.back_transcribe(seq)
-
def ungap(seq):
"""given a sequence with gap encoding, return the ungapped sequence"""
#TODO - Fix this? It currently assumes the outmost AlphabetEncoder
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6 DEPRECATED
@@ -329,3 +329,9 @@ Bio.SCOP
========
The module Bio.SCOP.FileIndex was deprecated in Release 1.46, and removed in
Release 1.53.
+
+Bio.utils
+=========
+The functions 'translate', 'translate_to_stop', 'back_translate', 'transcribe',
+and 'back_transcribe' were deprecated in Release 1.49, and removed in Release
+1.53.

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