table-five 0.0.2

No project description provided

fifteen

(DBA table_five)

Experimental library for quick quintet tallying, useful when you have a lot of quintets that somehow you don't want to count yourself.

Usage

Binary wheels are provided on PyPI

python3 -m pip install table_five

API

TreeSet

A treeset is an efficient (i.e., fast parsing) list of tree topologies. The construction is $O(k n \lg n)$ where $k$ is the number of trees and $n$ the number of taxa due to the LCA data structure initialization.

from table_five import TreeSet
trees = TreeSet("path_to_newline_delimited_newicks.tre")

Quintet Counting

The major API is tally_sinlge_quintet returning a list of length 15 containing the empirical counts of the 15 ADR unrooted quintet topology among the tree-set in $O(k)$ time:

# get counts of the ADR unrooted quintet topologies on taxa '1','2','3','4','5'. Taxa order matters.
treeset.tally_single_quintet(('1','2','3','4','5'))
# obviously you might want to convert it to numpy arrays

# normalize by the number of genes in the tree-set
new_tree_dist = np.asarray(treeset.tally_single_quintet(q_taxa)) / len(treeset)