1.5. Converting Between Data Formats

Any data in a schema that can be read by DendroPy, can be saved to files in any schema that can be written by DendroPy. Converting data between formats is simply a matter of calling readers and writers of the appropriate type.

Converting from FASTA schema to NEXUS:

>>> import dendropy
>>> cytb = dendropy.DnaCharacterMatrix.get_from_path("pythonidae_cytb.fasta", "dnafasta")
>>> cytb.write_to_path("pythonidae_cytb.nexus", "nexus")

Converting a collection of trees from NEXUS schema to Newick:

>>> import dendropy
>>> mcmc = dendropy.TreeList.get_from_path("pythonidae.mcmc.nex", "nexus")
>>> mcmc.write_to_path("pythonidae.mcmc.newick", "newick")

Converting a single tree from Newick schema to NEXUS:

>>> import dendropy
>>> mle = dendropy.Tree.get_from_path("pythonidae.mle.newick", "newick")
>>> mle.write_to_path("pythonidae.mle.nex", "nexus")

Collecting data from multiple sources and writing to a NEXUS-formatted file:

>>> import dendropy
>>> ds = dendropy.DataSet()
>>> ds.read_from_path("pythonidae_cytb.fasta", "dnafasta")
>>> ds.read_from_path("pythonidae_aa.nex", "nexus", taxon_set=ds.taxon_sets[0])
>>> ds.read_from_path("pythonidae_morphological.nex", "nexus", taxon_set=ds.taxon_sets[0])
>>> ds.read_from_path("pythonidae.mle.tre", "nexus", taxon_set=ds.taxon_sets[0])
>>> ds.write_to_path("pythonidae_combined.nex", "nexus")

Note how, after the first data source has been loaded, the resulting TaxonSet (i.e., the first one) is passed to the subsequent read_from_path statements, to ensure that the same taxa are referenced as objects corresponding to the additional data sources are created. Otherwise, as each data source is read, a new TaxonSet will be created, and this will result in multiple TaxonSet objects in the DataSet, with the data from each data source associated with their own, distinct TaxonSet.

A better way to do this is to use the “attached taxon set” mode DataSet object:

>>> import dendropy
>>> ds = dendropy.DataSet(attached_taxon_set=True)
>>> ds.read_from_path("pythonidae_cytb.fasta", "dnafasta")
>>> ds.read_from_path("pythonidae_aa.nex", "nexus")
>>> ds.read_from_path("pythonidae_morphological.nex", "nexus")
>>> ds.read_from_path("pythonidae.mle.tre", "nexus")
>>> ds.write_to_path("pythonidae_combined.nex", "nexus")