def main():
"""Simulate gene trees according to gene and lineage variation.
Modify the site variation by gene by simulating different alpha values.
also modify the clock for each site partition.
"""
params = variation.Settings()
base_tree = variation.relaxed_tree(
mod.get_file_data("../timetree.nwk")[0], 1, params.lineage_sigma2)
i = 0
trees = []
alphas = []
while i < 70:
relaxed_trees = []
rate = variation.get_rate(params.gene_alpha, params.gene_beta)
j = 0
while j < params.n_bins_per_gene:
relaxed_trees.append(
variation.relaxed_tree(base_tree, rate, params.lineage_sigma2))
j += 1
trees.append(relaxed_trees)
alphas.append(
str(variation.get_rate(params.site_alpha, params.site_alpha)))
i += 1
out_trees = open("treefiles.nwk", "w")
for set_of_trees in trees:
out_trees.write("\t".join(set_of_trees) + "\n")
out_trees.close()
out_alpha = open("alphas.txt", "w")
out_alpha.write("\n".join(alphas))
out_alpha.close()
def main():
"""Modify the 70 gene trees using simulated rates."""
base_tree = mod.get_file_data("../timetree.nwk")[0]
params = variation.Settings()
i = 0
while i < 70:
rate = variation.get_rate(params.gene_alpha, params.gene_beta)
new_tree = variation.modified_tree(base_tree, rate)
out = open("treefiles.nwk", "a+")
out.write(new_tree + "\n")
out.close()
i += 1
def main():
"""Write gene trees to a file."""
base_tree = mod.get_file_data("../timetree.nwk")[0]
params = variation.Settings()
rate = 1
tree = variation.relaxed_tree(base_tree, rate, params.lineage_sigma2)
out = open("treefiles.nwk", "a+")
i = 0
while i < 70:
out.write(tree + "\n")
i += 1
out.close()
def main():
"""Generate gene trees and write to a file."""
base_tree = mod.get_file_data("../timetree.nwk")[0]
params = variation.Settings()
rate = 1
tree = variation.relaxed_tree(base_tree, rate, params.lineage_sigma2)
out = open("treefiles.nwk", "a+")
i = 0
while i < 70:
rate = variation.get_rate(params.gene_alpha, params.gene_beta)
new_tree = variation.modified_tree(tree, rate)
out.write(new_tree + "\n")
i += 1
out.close()
def main():
"""Simulate gene trees according to gene variation.
Modify the site variation by gene by simulating different alpha values.
"""
base_tree = mod.get_file_data("../timetree.nwk")[0]
params = variation.Settings()
i = 0
trees = []
alphas = []
while i < 70:
rate = variation.get_rate(params.gene_alpha, params.gene_beta)
trees.append(variation.modified_tree(base_tree, rate))
alphas.append(str(variation.get_rate(params.site_alpha, params.site_alpha)))
i += 1
out_trees = open("treefiles.nwk", "w")
out_trees.write("\n".join(trees))
out_trees.close()
out_alpha = open("alphas.txt", "w")
out_alpha.write("\n".join(alphas))
out_alpha.close()
def main():
"""Simulate gene trees for genes with gene + lineage + sitexlineage variation.
This will involve a base tree for each bin per gene
each gene will have these trees for each partition multiplied by
the gene rate"""
base_tree = mod.get_file_data("../timetree.nwk")[0]
params = variation.Settings()
out = open("treefiles.nwk", "w")
relaxed_trees = []
i = 0
while i < 70:
j = 0
rate = variation.get_rate(params.gene_alpha, params.gene_beta)
while j < params.n_bins_per_gene:
relaxed_trees.append(
variation.relaxed_tree(base_tree, rate, params.lineage_sigma2))
j += 1
out.write("\t".join(relaxed_trees) + "\n")
i += 1
out.close()