[Biopython-dev] [Biopython] Alignment object

Peter biopython at maubp.freeserve.co.uk
Wed Oct 28 12:52:28 UTC 2009

On Wed, Oct 28, 2009 at 12:18 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> My rough work in progress in on github - at the moment I'm still trying
>> things out, and don't assume anything is set in stone. If you want to
>> have a play with this code, feedback is very welcome - probably best
>> on the dev list rather than here. See:
>> http://github.com/peterjc/biopython/tree/seqrecords
>> (a lot of the alignment things I want to support, like slicing and adding
>> are very closely linked to doing the same operations to SeqRecords)
> The bx-python alignment object is nice and goes to/from MAF and AXT
> formats:
> http://bitbucket.org/james_taylor/bx-python/src/tip/lib/bx/align/core.py
> This supports slicing by alignment coordinates and by reference
> coordinates for a species in the alignment. Some other useful
> features are limiting the alignment to specific species and removing
> all gap columns that can result. The representation is a high level
> Alignment object containing multiple Components.
> You can also index the files for quick lookup via range queries:
> http://bitbucket.org/james_taylor/bx-python/src/tip/lib/bx/interval_index_file.py
> http://bcbio.wordpress.com/2009/07/26/sorting-genomic-alignments-using-python/
> It's a nice implementation; it would be good to stay compatible with it and leverage
> as much as we can from what they've done.

We also have to try and stay compatible with the existing Biopython
alignment object though. But thanks for the bx links, I should take a


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