[Biopython-dev] MAF Parser/Writer/Indexer

[Sczesnak, Andrew]

> With something like SAM/BAM (or other assembly formats like ACE or the
> MIRA alignment format also called MAF), you can have multiple
> alignments (the contigs or chromosomes) each with many entries
> (supporting reads). Here there is a clear single reference coordinate
> system, that of the (gapped) reference contigs/chromosomes. This also
> means each alignment has a clear name (the name of the reference
> contig/chromosome), so this name and coordinates can be used for
> indexing (as in samtools).
>
> With MAF however, things are not so easy - any of the sequences could
> be used as a reference (e.g. human chr 1, or mouse chr 2), and any
> region of a sequence might be in more than one alignment.
>
> I'm beginning to suspect what Andrew has in mind is going to be MAF
> specific - so it won't be top level functionality in Bio.AlignIO, but
> rather tucked away in Bio.AlignIO.MafIO instead.
>
> Peter

I agree, the fact that this particular format does not explicitly define the
reference sequence is problematic.  Based on the spec, we ought to be 
prepared for a multiz MAF file with several different reference sequences.
However, practically speaking, the files out there in the world _do_ have a
reference sequence, which appears in all alignments and is the first listed
sequence.  While I think there is definitely some trickyness to how this
parser will have to interact with any API, my feeling is that these portions
ought to be confined to MafIO, while a more general API lives in AlignIO or
elsewhere.  This isn't much different from a format like SFF, I think.


Andrew

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