/usr/lib/R/site-library/phyloseq/extdata/gp500-pycogent.py is in r-bioc-phyloseq 1.22.3-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | # python/pycogent code to create reference UniFrac results for unit testing.
# Obviously, assumes that pycogent has generated correct values as well.
#
from cogent.maths.unifrac.fast_unifrac import fast_unifrac_file
import numpy
envs_in = open("inst/extdata/gp500test.env.txt")
tree_in = open("inst/extdata/gp500test.tree")
res_uuf = fast_unifrac_file(tree_in, envs_in, weighted=False)
numpy.savetxt("inst/extdata/gp500-uuf.csv", res_uuf['distance_matrix'][0], delimiter=",")
# Now wuf-unnormalized
envs_in = open("inst/extdata/gp500test.env.txt")
tree_in = open("inst/extdata/gp500test.tree")
res_wufu = fast_unifrac_file(tree_in, envs_in, weighted=True)
numpy.savetxt("inst/extdata/gp500-wufu.csv", res_wufu['distance_matrix'][0], delimiter=",")
# Now wuf (normalized... weighted='correct')
envs_in = open("inst/extdata/gp500test.env.txt")
tree_in = open("inst/extdata/gp500test.tree")
res_wuf = fast_unifrac_file(tree_in, envs_in, weighted='correct')
numpy.savetxt("inst/extdata/gp500-wuf.csv", res_wuf['distance_matrix'][0], delimiter=",")
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