Open jhcepas opened 9 years ago
I will work on the biopython side, something like biopythontree.to_ete()
thanks @jwillis0720, please keep us posted of any progress
@jwillis0720 is there only one Tree Instance type in BioPython? i.e. nexus, newick, nexml parsers always return the same instance type?
@jhcepas The tree instances are separate for different parsers. I would like to help with this if possible.
great, there have been no progress on this front for a long time. do you have any idea about implementation?
I am thinking of creating an API which can take the Tree Instance from Biopython and can conduct inter-conversion. I am thinking of working on Bio.Nexus
, Bio.CDAO
and then maybe move to PhyloXML
@jhcepas What are your thoughts on this?
@souravsingh sounds good. You can based your code on the scikit-bio loader. Or, if no other features are included in the Biopython tree rather than name and branch lengths, you could even load into ete by serialising the newick.
something like
Tree.from_biopython(...)
andTree.as_biopython(...)
1) The method should accept/return biopython Tree instances. 2) Is it possible to avoid newick serialisation? 3) any special attributes in Biopython Trees that need to be converted? 4) support for alignment objects? 5) any idea or feature request for a better integration between packages?