Adding missing copyright header (based on CVS log this was Andrew's w…

…ork). Deprecating the translation and transcription functions (use Bio.Seq instead)

Bio/utils.py

@@ -1,10 +1,25 @@
+# Copyright 2000 by Andrew Dalke.
+# All rights reserved.
+# 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.
+
+"""Miscellaneous functions for dealing with sequences (obsolete?)."""
+
 import string
 import Seq
 import Alphabet
 
 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:
@@ -13,6 +28,13 @@ def translate(seq, id = None):
     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:
@@ -21,6 +43,12 @@ def translate_to_stop(seq, id = None):
     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:
@@ -30,15 +58,31 @@ def back_translate(seq, id = None):
 
 
 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
+    #is for the gap.  Consider HasStopCodon(Gapped(Protein())) as a test case.
     gap = seq.gap_char
     letters = []
     for c in seq.data:
@@ -66,12 +110,12 @@ def count_monomers(seq):
     return dict
 
 def percent_monomers(seq):
-   dict2 = {}
-   seq_len = len(seq)
-   dict = count_monomers(seq)
-   for m in dict:
-      dict2[m] = dict[m] * 100. / seq_len
-   return dict2
+    dict2 = {}
+    seq_len = len(seq)
+    dict = count_monomers(seq)
+    for m in dict:
+        dict2[m] = dict[m] * 100. / seq_len
+    return dict2
 
 def sum(seq, table, zero = 0.0):
     total = zero