Missing taxonomic data in GreenGenes February 4, 2011 (referenced in supplementary information as source)

KoslickiLab / L2-UniFrac

Expansion upon Median Unifrac to compute average phylogenetic distances between samples according to their UniFrac distance without producing negative abundance vectors.

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Missing taxonomic data in GreenGenes February 4, 2011 (referenced in supplementary information as source) #3

Closed andrew-j-millward closed 3 years ago

andrew-j-millward commented 3 years ago

https://github.com/KoslickiLab/L2-UniFrac/blob/6fba0affc72c1efe98d18eee83ba0c63c2d2ac59/scripts/main.py#L12-L13

We get many of the following warnings from these two lines: "Warning: environments contain taxa ###### not present in given taxonomic tree. Ignoring" "../src\L2Unifrac.py:194: UserWarning: Warning: the sample *** has non-zero counts, do not use for Unifrac calculations warnings.warn("Warning: the sample %s has non-zero counts, do not use for Unifrac calculations" % sample)"

andrew-j-millward commented 3 years ago

Solved by removing date restriction on GreenGenes source and using most up-to-date tree file.