Tiding up some warnings, and deprecating Bio.utils.ungap() function

biopython · Nov 23, 2009 · 3e28b88 · 3e28b88
1 parent a8dea70
commit 3e28b88
Showing 1 changed file with 24 additions and 18 deletions.
diff --git a/Bio/utils.py b/Bio/utils.py
@@ -14,10 +14,10 @@
 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.",
+    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"
@@ -29,10 +29,10 @@ def translate(seq, id = None):
 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.",
+    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"
@@ -44,9 +44,9 @@ def translate_to_stop(seq, id = None):
 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.",
+    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"
@@ -59,10 +59,10 @@ 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.",
+    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)
@@ -71,9 +71,9 @@ 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.",
+                  " 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)
@@ -82,6 +82,12 @@ 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.
+    import warnings
+    warnings.warn("Bio.utils.ungap() has been deprecated, and we"
+                  " intend to remove it in a future release of Biopython."
+                  " Instead, please use the ungap method of the Seq object "
+                  " (added in Biopython 1.53).",
+                  DeprecationWarning)
     gap = seq.gap_char
     letters = []
     for c in seq.data: