[Biopython-dev] [Bug 2731] Adding .upper() and .lower() methods to the Seq object

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2731





------- Comment #1 from bsouthey at gmail.com  2009-01-12 17:43 EST -------
(In reply to comment #0)
> As part of making the Seq object more string like (Bug 2351), it would be nice
> to support the .upper() and .lower() methods.

Sure it would be nice in terms of following the string object, but I do not
follow the reasons for having .upper() and .lower() methods to the Seq object.
If we follow the standards, these should be unnecessary. The only time that I
see is when you want this is to output the sequence. In such situations, the
sequence is likely to be a string which has these methods.

I do not consider that other applications can handle different case a
sufficiently compelling reason.

> 
> Doing this elegantly will require different case versions of the alphabets (see
> Bug 2532), perhaps by adding (private) upper and lower methods to the Alphabet
> object itself.
> 
> Alternatively, we can handle this without adding new Alphabets by mapping the
> fixed case IUPAC alphabets to case-less generic alphabets.
> 

These comments suggests that Seq object needs to be case-aware which also
affects other methods like string queries. But I think this is a different
issue such as whether or not the standards would be enforced than having these
two methods. 

Bruce


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