Case Sensitive Taxon Names — Bug?

[Eric Q. Miller]

Hello, 

According to the documentation, in order to allow case sensitive taxon names (e.g. 'Streptococcus' and 'streptococcus') in DendroPy, case_insensitive_taxon_labels should be set to false (https://github.com/jeetsukumaran/DendroPy/blob/master/doc/source/tutorial/taxa.rst):

tree = dendropy.Tree.get_from_path("\pathname", schema = "newick", case_insensitive_taxon_labels = False)

The command above does not work (given a correct pathname).

In looking at the code, what works for me is instead:

tree = dendropy.Tree.get_from_path("\pathname", schema = "newick", case_sensitive_taxon_labels=True)

I just wanted to post a message so that if anyone else gets a bit stuck from this.

I encountered the problem because my taxa are given systematic letter combinations (e.g. "Aab", "AAb", "AaB"), which when encountered, DendroPy reports a helpful error message that pointed me into the correct direction.

Cheers,

Eric

[Jeet Sukumaran]

Hi Eric,

Yes, the documentation needs to be fixed. Thanks for pointing it out,
and thanks for the trouble to sharing your findings with the community.

Actually, version 3 of the library is a little inconsistent with places
where it uses "case_sensitive = True/False" vs. "case_insensitive =
True/False" in various method and function signatures. This can
definitely be annoying, especially when the documentation is in error
with regards to this like you point out.

In DendroPy4, which we are reworking through line-by-line, we are
streamlining all signatures to go with the "case_sensitive=True/False"
approach:


https://github.com/jeetsukumaran/DendroPy/blob/DendroPy4/doc/source/migration.rst

-- jeet

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