[Biopython-dev] [Bug 1944] Align.Generic adding iterator and more

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http://bugzilla.open-bio.org/show_bug.cgi?id=1944





------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2007-09-25 18:19 EST -------
Created an attachment (id=768)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=768&action=view)
Replacement Bio/Align/__init__.py (alignment update v4)

This is based on attachment 732, my 3rd version of a patch to
Bio/Align/Generic.py but handled as new alignment class in
Bio/Align/__init__.py

This implements a new alignment class which:
* directly subclasses the python list (as a list of SeqRecords)
* allows flexible subscripting using __getitem__
* enforces strict alphabet and length checking in __init__, append and extend

There is plenty more polish needed - including tackling tricky questions like
__setitem__ (or __setslice__) and the related questions about editing
alignments.

As per my comment 10, I would like to get SeqRecord to support splicing giving
SeqRecords with (partial) annotation.  If this is done, then the alignment
class can exploit this (i.e. only have one set of code dealing with the
annotation when splicing SeqRecords).  Right now only the id/name/description
are preserved when splicing alignments.


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