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Also deprecate AlignACE & CompareACE wrappers in Bio.motifs

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commit e949ff11cc9cca5aa2d8b1a0e7d09d2760f4a21b 1 parent 0a11407
Peter Cock authored July 08, 2013

Showing 1 changed file with 17 additions and 4 deletions. Show diff stats Hide diff stats

  1. 21  Bio/motifs/applications/_alignace.py
21  Bio/motifs/applications/_alignace.py
@@ -25,9 +25,12 @@
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 """
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 from Bio.Application import AbstractCommandline, _Option, _Argument
27 27
 
  28
+import warnings
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+from Bio import BiopythonDeprecationWarning
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+
28 31
 
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 class AlignAceCommandline(AbstractCommandline):
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-    """Create a commandline for the AlignAce program.
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+    """Create a commandline for the AlignAce program (DEPRECATED).
31 34
 
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     Example:
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@@ -41,6 +44,12 @@ class AlignAceCommandline(AbstractCommandline):
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     the Python subprocess module, as described in the Biopython tutorial.
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     """
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     def __init__(self, cmd="AlignACE", **kwargs):
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+        warnings.warn("""The AlignACE application wrapper is deprecated and
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+                      is likely to be removed in a future release of Biopython,
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+                      since an up to date version of the AlignACE software
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+                      cannot be obtained anymore. If you have a copy of
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+                      AlignACE 4, please consider contacting the Biopython
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+                      developers.""", BiopythonDeprecationWarning)
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         self.parameters = \
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           [
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             _Option(["-i", "infile"],
@@ -103,8 +112,12 @@ class CompareAceCommandline(AbstractCommandline):
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     the Python subprocess module, as described in the Biopython tutorial.
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     """
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     def __init__(self, cmd="CompareACE", **kwargs):
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-        import os.path
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-
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+        warnings.warn("""The CompareACE application wrapper is deprecated and
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+                      is likely to be removed in a future release of Biopython,
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+                      since an up to date version of the AlignACE software
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+                      cannot be obtained anymore. If you have a copy of
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+                      AlignACE 4, please consider contacting the Biopython
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+                      developers.""", BiopythonDeprecationWarning)
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         self.parameters = \
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           [
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             _Argument(["motif1"],
@@ -121,7 +134,7 @@ def __init__(self, cmd="CompareACE", **kwargs):
121 134
 
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 def _test():
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     """Run the module's doctests (PRIVATE)."""
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-    print "Running AlignAce doctests..."
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+    print "Running alignace doctests..."
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     import doctest
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     doctest.testmod()
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     print "Done"

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