[Biopython] Ace support in Bio.SeqIO and/or Bio.AlignIO?

[Peter]

How do you picture a contig in an ACE assembly file? As a single
record with read data annotations (e.g. as a SeqRecord), or as a
sequence alignment with a consensus (e.g. as an Alignment object)?  I
suspect the answer is "it depends", and that both are useful.

Currently we use Bio.Sequencing.Ace in Bio.SeqIO to turn each contig
into a SeqRecord.  Now that we have per-letter-annotation support in
the SeqRecord, this code could be updated to record the consensus base
quality (BQ lines).  We could also record the supporting reads (RD
lines), maybe as SeqFeature objects.

Recently David put together an example on the wiki using
Bio.Sequencing.Ace to build an alignment, which we could use a basis
for supporting Ace files in Bio.AlignIO as alignments:
http://biopython.org/wiki/ACE_contig_to_alignment

What do people think?  I should be able to try out David's code on
some real world ACE files from Newbler (i.e. 454Contigs.ace files)...

Peter