Coverage for Bio.GenBank.utils : 44%

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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. #
"""
"""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). """
"""Initialize with the keys we should deal with. """
"""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
"""Concatenate a translation value to one long protein string. """ translation_parts = value.split() return "".join(translation_parts) |