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python-biopython  1.60
__init__.py
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00001 # Copyright 2000 by Jeffrey Chang.  All rights reserved.
00002 # This code is part of the Biopython distribution and governed by its
00003 # license.  Please see the LICENSE file that should have been included
00004 # as part of this package.
00005 """Collection of modules for dealing with biological data in Python.
00006 
00007 The Biopython Project is an international association of developers 
00008 of freely available Python tools for computational molecular biology.
00009 
00010 http://biopython.org
00011 """
00012 
00013 __docformat__ = "epytext en" #not just plaintext
00014 
00015 __version__ = "1.60"
00016 
00017 class MissingExternalDependencyError(Exception):
00018     """Missing an external dependency.
00019 
00020     Used for things like missing command line tools. Important for our unit
00021     tests to allow skipping tests with missing external dependencies.
00022     """
00023     pass
00024 
00025 class MissingPythonDependencyError(MissingExternalDependencyError, ImportError):
00026     """Missing an external python dependency (subclass of ImportError).
00027 
00028     Used for missing Python modules (rather than just a typical ImportError).
00029     Important for our unit tests to allow skipping tests with missing external
00030     python dependencies, while also allowing the exception to be caught as an
00031     ImportError.
00032     """
00033     pass
00034 
00035 class BiopythonWarning(Warning):
00036     """Biopython warning.
00037     
00038     Biopython should use this warning (or subclasses of it), making it easy to
00039     silence all our warning messages should you wish to:
00040 
00041         >>> import warnings
00042         >>> from Bio import BiopythonWarning
00043         >>> warnings.simplefilter('ignore', BiopythonWarning)
00044 
00045     Consult the warnings module documentation for more details.
00046     """
00047     pass
00048 
00049 class BiopythonParserWarning(BiopythonWarning):
00050     """Biopython parser warning.
00051     
00052     Some in-valid data files cannot be parsed and will trigger an exception.
00053     Where a reasonable interpretation is possible, Biopython will issue this
00054     warning to indicate a potential problem. To silence these warnings, use:
00055 
00056         >>> import warnings
00057         >>> from Bio import BiopythonParserWarning
00058         >>> warnings.simplefilter('ignore', BiopythonParserWarning)
00059 
00060     Consult the warnings module documentation for more details.
00061     """
00062     pass
00063 
00064 class BiopythonDeprecationWarning(BiopythonWarning):
00065     """Biopython deprecation warning.
00066     
00067     Biopython uses this warning instead of the built in DeprecationWarning
00068     since those are ignored by default since Python 2.7.
00069 
00070     To silence all our deprecation warning messages, use:
00071 
00072         >>> import warnings
00073         >>> from Bio import BiopythonDeprecationWarning
00074         >>> warnings.simplefilter('ignore', BiopythonDeprecationWarning)
00075 
00076     Code marked as deprecated is likely to be removed in a future version
00077     of Biopython. To avoid removal of this code, please contact the Biopython
00078     developers by sending an email to biopython-dev@biopython.org.
00079     """
00080     pass