Bio package

Subpackages

Module contents

Collection of modules for dealing with biological data in Python.

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

https://biopython.org

exception Bio.MissingExternalDependencyError

Bases: Exception

Missing an external dependency.

Used for things like missing command line tools. Important for our unit tests to allow skipping tests with missing external dependencies.

exception Bio.MissingPythonDependencyError

Bases: Bio.MissingExternalDependencyError, ImportError

Missing an external python dependency (subclass of ImportError).

Used for missing Python modules (rather than just a typical ImportError). Important for our unit tests to allow skipping tests with missing external python dependencies, while also allowing the exception to be caught as an ImportError.

exception Bio.StreamModeError

Bases: ValueError

Incorrect stream mode (text vs binary).

This error should be raised when a stream (file or file-like object) argument is in text mode while the receiving function expects binary mode, or vice versa.

exception Bio.BiopythonWarning

Bases: Warning

Biopython warning.

Biopython should use this warning (or subclasses of it), making it easy to silence all our warning messages should you wish to:

>>> import warnings
>>> from Bio import BiopythonWarning
>>> warnings.simplefilter('ignore', BiopythonWarning)

Consult the warnings module documentation for more details.

exception Bio.BiopythonParserWarning

Bases: Bio.BiopythonWarning

Biopython parser warning.

Some in-valid data files cannot be parsed and will trigger an exception. Where a reasonable interpretation is possible, Biopython will issue this warning to indicate a potential problem. To silence these warnings, use:

>>> import warnings
>>> from Bio import BiopythonParserWarning
>>> warnings.simplefilter('ignore', BiopythonParserWarning)

Consult the warnings module documentation for more details.

exception Bio.BiopythonDeprecationWarning

Bases: Bio.BiopythonWarning

Biopython deprecation warning.

Biopython uses this warning instead of the built in DeprecationWarning since those are ignored by default since Python 2.7.

To silence all our deprecation warning messages, use:

>>> import warnings
>>> from Bio import BiopythonDeprecationWarning
>>> warnings.simplefilter('ignore', BiopythonDeprecationWarning)

Code marked as deprecated is likely to be removed in a future version of Biopython. To avoid removal of this code, please contact the Biopython developers via the mailing list or GitHub.

exception Bio.BiopythonExperimentalWarning

Bases: Bio.BiopythonWarning

Biopython experimental code warning.

Biopython uses this warning for experimental code (‘alpha’ or ‘beta’ level code) which is released as part of the standard releases to mark sub-modules or functions for early adopters to test & give feedback.

Code issuing this warning is likely to change (or even be removed) in a subsequent release of Biopython. Such code should NOT be used for production/stable code. It should only be used if:

  • You are running the latest release of Biopython, or ideally the latest code from our repository.

  • You are subscribed to the biopython-dev mailing list to provide feedback on this code, and to be alerted of changes to it.

If all goes well, experimental code would be promoted to stable in a subsequent release, and this warning removed from it.