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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Useful utilities for helping in parsing GenBank files.
"""
class FeatureValueCleaner(object):
"""Provide specialized capabilities for cleaning up values in features.
This class is designed to provide a mechanism to clean up and process
values in the key/value pairs of GenBank features. This is useful
because in cases like:
/translation="MED
YDPWNLRFQSKYKSRDA"
you'll end up with a value with \012s and spaces in it like:
"MED\012 YDPWEL..."
which you probably don't want.
This cleaning needs to be done on a case by case basis since it is
impossible to interpret whether you should be concatenating everything
(as in translations), or combining things with spaces (as might be
the case with /notes).
"""
keys_to_process = ["translation"]
def __init__(self, to_process = keys_to_process):
"""Initialize with the keys we should deal with.
"""
self._to_process = to_process
def clean_value(self, key_name, value):
"""Clean the specified value and return it.
If the value is not specified to be dealt with, the original value
will be returned.
"""
if key_name in self._to_process:
try:
cleaner = getattr(self, "_clean_%s" % key_name)
value = cleaner(value)
except AttributeError:
raise AssertionError("No function to clean key: %s"
% key_name)
return value
def _clean_translation(self, value):
"""Concatenate a translation value to one long protein string.
"""
translation_parts = value.split()
return "".join(translation_parts)
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