def test_solve_inc(self):
m_eval, c_eval, k1_eval, tree_eval = phyl.solve_incomplete_phylogeny(m1,s1,c1)
k1 = phyl.get_k1_matrix(m_eval,c_eval)
self.assertTrue(np.all(m_exp==m_eval))
self.assertTrue(np.all(k1_exp==k1_eval))
self.assertTrue(np.all(tree_exp==tree_eval))
self.assertTrue(phyl.perfect_phylogeny_exists(k1,c_eval))
def test_solve_inc(self):
m_eval, c_eval, k1_eval, tree_eval = phyl.solve_incomplete_phylogeny(
m1, s1, c1)
k1 = phyl.get_k1_matrix(m_eval, c_eval)
self.assertTrue(np.all(m_exp == m_eval))
self.assertTrue(np.all(k1_exp == k1_eval))
self.assertTrue(np.all(tree_exp == tree_eval))
self.assertTrue(phyl.perfect_phylogeny_exists(k1, c_eval))
'''
import argparse
import numpy as np
from perfect_phylogeny import phylogeny as phyl
parser = argparse.ArgumentParser(prefix_chars='--')
parser.add_argument('m_file',help='Matrix file')
parser.add_argument('outname',nargs='?',default='tree',help='Output name')
parser.add_argument('--plot',dest='plot',action='store_true',help='Plot output (if valid phylogeny). Requires Graphviz.')
args = parser.parse_args()
m_file = args.m_file
outname = args.outname
plot = args.plot
if __name__ == '__main__':
m_txt = np.genfromtxt(m_file,delimiter='\t',dtype=None,invalid_raise=False)
s = np.array(m_txt[1:,0],dtype='S100') # row names/samples
c = np.array(m_txt[0,1:],dtype='S100') # column names/features
m = np.array(m_txt[1:,1:],dtype=int) # matrix values
m_new, c_prime, k1, tree = phyl.solve_incomplete_phylogeny(m,s,c)
k1 = phyl.get_k1_matrix(m_new,c_prime)
if phyl.perfect_phylogeny_exists(k1,c_prime) and plot:
print('Plotting tree...')
phyl.write_dot(k1,s,outname)
def test_no_phyl(self):
m_eval, c_eval = phyl.get_m_prime(m2,c2)
k1 = phyl.get_k1_matrix(m_eval,c_eval)
self.assertTrue(np.all(k1_nophyl==k1))
self.assertFalse(phyl.perfect_phylogeny_exists(k1,c_eval))
parser.add_argument('m_file', help='Matrix file')
parser.add_argument('outname', nargs='?', default='tree', help='Output name')
parser.add_argument(
'--plot',
dest='plot',
action='store_true',
help='Plot output (if valid phylogeny). Requires Graphviz.')
args = parser.parse_args()
m_file = args.m_file
outname = args.outname
plot = args.plot
if __name__ == '__main__':
m_txt = np.genfromtxt(m_file,
delimiter='\t',
dtype=None,
invalid_raise=False)
s = np.array(m_txt[1:, 0], dtype='S100') # row names/samples
c = np.array(m_txt[0, 1:], dtype='S100') # column names/features
m = np.array(m_txt[1:, 1:], dtype=int) # matrix values
m_new, c_prime, k1, tree = phyl.solve_incomplete_phylogeny(m, s, c)
k1 = phyl.get_k1_matrix(m_new, c_prime)
if phyl.perfect_phylogeny_exists(k1, c_prime) and plot:
print('Plotting tree...')
phyl.write_dot(k1, s, outname)
def test_no_phyl(self):
m_eval, c_eval = phyl.get_m_prime(m2, c2)
k1 = phyl.get_k1_matrix(m_eval, c_eval)
self.assertTrue(np.all(k1_nophyl == k1))
self.assertFalse(phyl.perfect_phylogeny_exists(k1, c_eval))