[Biopython-dev] [Bug 2551] Adding advanced __getitem__ to generic alignment, e.g. align[1:2, 5:-5]

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2551





------- Comment #2 from jblanca at btc.upv.es  2008-09-30 08:55 EST -------
In the comment #1 I present a class that could be easily adapted to be
compatible with the BioPython Alignment API but with some extra capabilities.
It can hold sequences that start and end at different places (like the EST
assemblies).
It also can have a consensus, although that's a minor improvement.
And it can hold in the rows any sequence-like class like Seq, str, list or
tuple. This would be, I hope, quite future proof, we could also add Quality,
SeqWithQuality or whatever.
It doesn't deal with the alphabet, I think that a subclass should be created to
add that capability. I haven't add alphabets to this class to keep the
compatibility with all the sequence-like objects that have no alphabet.


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