[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 #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-15 12:39 EST -------
Until recently we supported only:

        align[r] gives a row as a SeqRecord

Updated in CVS to support row-slicing:

        align[start:end:step] gives a new (sub)alignment

e.g.
align[1:5] - new four row sub-alignment
align[::2] - sub alignment using every second row
align[:] - makes a copy
align[::-1] - makes a copy with the row order reversed

The current implementation could be improved after fixing enhancement Bug 2554.

This leaves the door open for double indexes as previously outlined (blocking
on Bug 2507).

--

In reply to Jose's comment 1 and comment 2, this really is a complete
replacement for the current alignment object, and would be better off on a
separate bug.


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