[Biopython-dev] MAF Parser/Writer/Indexer
Andrew Sczesnak
andrew.sczesnak at med.nyu.edu
Mon May 16 17:26:46 UTC 2011
On 05/16/2011 07:14 AM, Peter Cock wrote:
> Do you think we should follow the speciesOrder directive if
> present?
Yeah, why not. I started working on this and the problem was, as
defined in the spec, the species is just "hg19" or "mm9," yet the
records are in species.chromosome format. Should we enforce that the
species in a speciesOrder directive must exactly match a sequence
identifier, or add a split and do some checks to make sure a record
matches only one species in speciesOrder?
> Also I think we may need to do something rigorous with start/end
> co-ordinates and strand in either the Seq or SeqRecord object.
> They could be updated automatically during slicing and taking
> reverse complement... they might not survive addition though.
This is interesting. I wonder if it makes sense to preserve this
information if a SeqRecord is going to be maniuplated outside a
MultipleSeqAlignment object. Could this be accomplished by migrating
the annotation information to a SeqFeature?
Andrew
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