[Biopython-dev] [Bug 1718] New: Fasta.Dictionary should support "in" (the __contains__ method)

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Dec 8 19:00:15 EST 2004


           Summary: Fasta.Dictionary should support "in" (the __contains__
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

With a real Python dictionary you can do this:

dictionary = {'A' : 'Apple', 'B' : 'Bananna', 'C' : 'Cherry'}
print 'A' in dictionary
print 'D' in dictionary

The Fasta.Dictionary does not support this.  It fails with a TypeError exception
from Mindy which is very confusing to a novice (full traceback below).

Possible implementation in Bio/Fasta/__init__.py is as follows:

    def __contains__(self, key) :
        """key in D -> True if D has a key k, else False
        return key in self._index['id'].keys()

A Mindy expert may have a more efficient way of doing this.


Traceback (most recent call last):
  File "C:\Temp\fasta_dict_bug\test.py", line 33, in ?
    print 'Alpha' in fasta_dict
  File "C:\Python23\lib\site-packages\Bio\Fasta\__init__.py", line 187, in
    seqs = self._index.lookup(id = key)
  File "c:\python23\Lib\site-packages\Bio\Mindy\BaseDB.py", line 118, in lookup
    return self[namespace][name]
  File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 329, in __getitem__
    loc = _lookup_location(self.db.key_filename, name)
  File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 258, in
    line = _find_entry(key_filename, word)
  File "c:\python23\Lib\site-packages\Bio\Mindy\FlatDB.py", line 235, in _find_entry
    if not line.startswith(wantword):
TypeError: expected a character buffer object


See also the related:
Bug 1716 - Fasta.Dictionary should throw KeyError for invalid keys
Bug 1717 - Fasta.Dictionary should support has_key

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