[Biopython-dev] [Bug 3066] New: Iterating/looping over colums/rows of a MultipleSeqAlignment

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3066

           Summary: Iterating/looping over colums/rows of a
                    MultipleSeqAlignment
           Product: Biopython
           Version: 1.54b
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


The new MultipleSeqAlignment object (like the old Alignment object it replaces)
stores the rows of the alignment as SeqRecord objects. This means column based
access is slow.

It can often be useful to be able to iterate over the columns, and a dedicated
method to do this should be faster than repeatedly accessing columns by index
(either via slicing with __getitem__ or the old get_column method).

A related question here is should the columns be returned as strings or as Seq
objects? Possible implementation to follow as a patch...


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