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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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interoperability with BioPython #138

Open jhcepas opened 9 years ago

jhcepas commented 9 years ago

something like Tree.from_biopython(...) and Tree.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?

jwillis0720 commented 9 years ago

I will work on the biopython side, something like biopythontree.to_ete()

jhcepas commented 8 years ago

thanks @jwillis0720, please keep us posted of any progress

jhcepas commented 8 years ago

@jwillis0720 is there only one Tree Instance type in BioPython? i.e. nexus, newick, nexml parsers always return the same instance type?

souravsingh commented 7 years ago

@jhcepas The tree instances are separate for different parsers. I would like to help with this if possible.

jhcepas commented 7 years ago

great, there have been no progress on this front for a long time. do you have any idea about implementation?

souravsingh commented 7 years ago

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

souravsingh commented 6 years ago

@jhcepas What are your thoughts on this?

jhcepas commented 6 years ago

@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.