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Description:
taxOrder 0.2.7
Package:
from taxOrder.taxOrder import order_taxa
taxorder = order_taxa(tree, 'Homo_sapiens', format=1, idmap='')
Command line implementation:
usage: taxOrder [-h] -t <path> -r str [--outfile [str]] [--format [str]] [--idmap [<path>]]
Returns list of species in a phylogenetic tree ordered by increasing taxonomic distance to a reference species
-h, --help show this help message and exit
-t <path>, --tree <path>
Path to tree in Newick format
-r , --reference str
Reference species
optional arguments:
--outfile [str] Save output to file
--format [str] Tree format as specified at: https://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees (Default: 1)
--idmap [<path>] TaxOrder can map species names to taxids accepted by PhyloProfile if supplied with a tab-seperated file like: taxid name
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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