[Biopython-dev] [Bug 2553] New: Adding SeqRecord objects to an alignment (append or extend)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2553

           Summary: Adding SeqRecord objects to an alignment (append or
                    extend)
           Product: Biopython
           Version: Not Applicable
          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


Currently a Bio.Align.Generic.Alignment object stores the rows as SeqRecord
objects, but only exposes a public API for adding row sequences as strings.

As suggested on Bug 1944, it would make sense to treat the Alignment as a list
of SeqRecord objects and therefore support the list methods .append() and
.extend() for the addition of more rows as SeqRecord objects.

I would make the .append() method enforce the expectation that all rows are the
same length, and that the new sequence's alphabet is compatible with the
declared alignment alphabet.

See also Bug 2552 - Adding alignments


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