[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


bsouthey at gmail.com changed:

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                 CC|                            |bsouthey at gmail.com




------- Comment #2 from bsouthey at gmail.com  2008-09-29 10:34 EST -------
(In reply to comment #1)
I do think that any general function involving regular expressions should
conform to the Python re module. The reasoning follows Peter's point that a
user should not have to convert the Seq object into a Python string. While I
see the point of the reverse complement and overlapping matches, these are
inconsistent with re module. So I think it would be more valuable to implement
specific methods from the re modules. In this case, the functions should accept
regular expression.

I also do not see the gain for the reverse complement because this is just
another pattern. Also it is potentially confusing because the direction is not
immediately apparent without further computation. In this case I think that
'explicit is better than implicit' (The Zen of Python) so I think the decision
to use the reverse complement must come prior to the use of this method.


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