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Move warning & update docstrings.

Warning from 'from Bio.Motif import Applications' not nice.
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1 parent 602f0cb commit 0a114072c43e431dfc4e08db2285bbf666ab6846 @peterjc peterjc committed Jul 8, 2013
Showing with 14 additions and 5 deletions.
  1. +14 −5 Bio/Motif/Applications/_AlignAce.py
@@ -27,11 +27,10 @@
import warnings
from Bio import BiopythonDeprecationWarning
-warnings.warn("The AlignACE/CompareACE application wrapper is deprecated and is likely to be removed in a future release of Biopython, since an up to date version of the AlignACE software cannot be obtained anymore. If you have a copy of AlignACE 4, please consider contacting the Biopython developers.", BiopythonDeprecationWarning)
class AlignAceCommandline(AbstractCommandline):
- """Create a commandline for the AlignAce program.
+ """Create a commandline for the AlignAce program (DEPRECATED).
Example:
@@ -45,6 +44,12 @@ class AlignAceCommandline(AbstractCommandline):
the Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="AlignACE", **kwargs):
+ warnings.warn("""The AlignACE application wrapper is deprecated and
+ is likely to be removed in a future release of Biopython,
+ since an up to date version of the AlignACE software
+ cannot be obtained anymore. If you have a copy of
+ AlignACE 4, please consider contacting the Biopython
+ developers.""", BiopythonDeprecationWarning)
self.parameters = \
[
_Option(["-i", "infile"],
@@ -92,7 +97,7 @@ def __init__(self, cmd="AlignACE", **kwargs):
class CompareAceCommandline(AbstractCommandline):
- """Create a commandline for the CompareAce program.
+ """Create a commandline for the CompareAce program (DEPRECATED).
Example:
@@ -107,8 +112,12 @@ class CompareAceCommandline(AbstractCommandline):
the Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="CompareACE", **kwargs):
- import os.path
-
+ warnings.warn("""The CompareACE application wrapper is deprecated and
+ is likely to be removed in a future release of Biopython,
+ since an up to date version of the AlignACE software
+ cannot be obtained anymore. If you have a copy of
+ AlignACE 4, please consider contacting the Biopython
+ developers.""", BiopythonDeprecationWarning)
self.parameters = \
[
_Argument(["motif1"],

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