[Biopython-dev] [Bug 2601] Seq find() method: proposal

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2601





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-09-29 09:24 EST -------
Note that any Seq.find() method should be as like the string find method as
possible for consistency.  One enhancement is that it might be worth checking
the search string is valid against the Seq object's alphabet (see also Bug
2597).

However, reserving Seq.find() for this string find like behaviour doesn't stop
us adding more advanced regular expression based methods.

P.S. To determine if a sequence has a nucleotide alphabet, use the fact that
any well defined nucleotide alphabet object should be a subclass of
Bio.Alphabet.NucleotideAlphabet() rather than checking a predefined list. 
However, there is no way of knowing if the sequence is double stranded or
single sided, so personally I don't like the way your suggested function
automatically searches the reverse complement strand too.


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