Sunday, June 19, 2011

A Change in Plan

So there is a change in plan here.

What I had thought earlier :-
Earlier I thought that a nwk and a csv file have to be completely replaced by a single NeXML file. While this may be the ultimate goal but at present this is not something which is possible. The reasons for it are as follows

1) There are no examples with location metadata attached to nodes in NeXML in TreeBase.
2) There is no preferred choice which is likely to be the manner in which coordinate metadata would be attached to the nodes in future.

So here is what the current plan is.

  1. INPUT 1: A nexml file with whatever metadata it has to offer.
  2. INPUT 2: A second file with additional metadata that you might want to attach to the nodes.
  3. Having taken both these files, construct a crude Phylogeny tree from the nexml file. By crude I mean to say that this phylogeny is incomplete. This phylogeny has the basic tree structure but it may not have all the essential metadata.
  4. Now extract the additional metadata from the second file and embed it in the phylogeny.
  5. You now get a full fledged Phylogeny with all the metadata.
In the earlier plan I was trying to stuff everything into the nexml first and then use this nexml to prepare the phylogeny tree. This had the overhead of first creating a modified nexml file with all the metadata and then preparing the phylogeny from it.
I will be writing the code in a manner that the user will have the option of choosing whether this second input file is to be taken as an input or not.

While preparing a fully fledged Phylogenetic tree from NeXML would be a utopia. What we do at present is that prepare a partially prepared Phylogenetic tree which I call as crude phylogenetic tree and then patch it with metadata from the other file.

Preparing a fully functional NeXML is now at the bottom of my priority list.

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