Nexus: taxa and format

[PhyloStar]

When LingPy generates a nexus files, some of the language names have characters such as space, parantheses where MrBayes complains. Another format is the length of the name field in the nexus file. You might want to consider to have a tab separated line such as:
GERMAN\t010101

[LinguList]

there's a better way for nexus output, but there's a bug for mrbayes, so you'll need to look into that or manually refine (or just ignore mrbayes commands):

• http://lingpy.org/news.html#adding-nexus-output

In general, I recommend changing language names in the data.

[PhyloStar]

Okay. I prefer glottolog codes or ASJP style names. Or the length of the name field to be fixed like 40 characters something like PHYLIP is also fine.

[LinguList]

In fact, I checked, and when using lingpy.convert.strings.pap2nex instead of the simple output, we can add the taxa:

>>> wl = Wordlist('example.tsv')
>>> from lingpy.convert.strings import pap2nex
>>> taxa = [myglottoconverter[t] for t in wl.taxa]
>>> paps = wl.get_paps(ref='cogid/infomapid/whatever', missing="?")
>>> pap2nex(taxa, paps, filename="outputfile")

[LinguList]

This is the same as wl.output(*) but you can specify the language names.

[PhyloStar]

Okay. This is great. Thank you.