[Biopython-dev] [Bug 2597] Enforce alphabet letters in Seq objects

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2597





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-22 12:38 EST -------
Created an attachment (id=1175)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1175&action=view)
Patch for Bio/Seq.py to check the alphabet letters

This is a simple approach to checking the letters - probably not the fastest. 
I think it is important that the exception gives some clue about why the Seq
object was not created - either listing the first invalid character (as in this
patch) or listing all invalid characters (which could be done using sets).

On the other hand, I'd like this check to be as fast as possible - perhaps even
at the cost of a generic exception message like "Sequence contains letters
which are not valid for the given alphabet".


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