Error messages when pydoc tries to search keywords through biopython module

biopython.txt (text/plain), 1.93 KB, created by David Suarez on 2010-04-04 19:43:54 UTC

$ pydoc -k TaggedList
Traceback (most recent call last):
  File "/usr/bin/pydoc", line 5, in <module>
    pydoc.cli()
  File "/usr/lib64/python2.6/pydoc.py", line 2272, in cli
    apropos(val)
  File "/usr/lib64/python2.6/pydoc.py", line 1967, in apropos
    ModuleScanner().run(callback, key)
  File "/usr/lib64/python2.6/pydoc.py", line 1932, in run
    for importer, modname, ispkg in pkgutil.walk_packages(onerror=onerror):
  File "/usr/lib64/python2.6/pkgutil.py", line 125, in walk_packages
    for item in walk_packages(path, name+'.', onerror):
  File "/usr/lib64/python2.6/pkgutil.py", line 110, in walk_packages
    __import__(name)
  File "/usr/lib64/python2.6/site-packages/Bio/GFF/__init__.py", line 49, in <module>
    raise MissingExternalDependencyError("Install MySQLdb if you want to use Bio.GFF.")
Bio.MissingExternalDependencyError: Install MySQLdb if you want to use Bio.GFF.
david@hostname ~ $ python
Python 2.6.4 (r264:75706, Mar  8 2010, 09:56:43) 
[GCC 4.3.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> import Bio.GFF
/usr/lib64/python2.6/site-packages/Bio/GFF/__init__.py:33: DeprecationWarning: The old Bio.GFF module for access to a MySQL GFF database created with BioPerl is deprecated, and will be removed (or possibly just moved) in a future release of Biopython.  If you want to continue to use this code, please get in contact with the developers via the mailing lists to avoid its permanent removal from Biopython. The plan is to re-use the Bio.GFF namespace for a new GFF parsing module.
  "namespace for a new GFF parsing module.", DeprecationWarning)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.6/site-packages/Bio/GFF/__init__.py", line 49, in <module>
    raise MissingExternalDependencyError("Install MySQLdb if you want to use Bio.GFF.")
Bio.MissingExternalDependencyError: Install MySQLdb if you want to use Bio.GFF.