def single_file_upgma(input_file, output_file):
# read in dist matrix
f = open(input_file, 'U')
headers, data = parse_distmat(f)
f.close()
# do upgma
nodes = map(PhyloNode, headers)
BIG = 1e305
U = data.copy()
for i in range(len(U)):
U[i,i] = BIG
c = UPGMA_cluster(U, nodes, BIG)
# write output
f = open(output_file,'w')
f.write(c.getNewick(with_distances=True))
f.close()
def single_file_upgma(input_file, output_file):
# read in dist matrix
f = open(input_file, 'U')
headers, data = parse_distmat(f)
f.close()
# do upgma
nodes = map(PhyloNode, headers)
BIG = 1e305
U = data.copy()
for i in range(len(U)):
U[i,i] = BIG
c = UPGMA_cluster(U, nodes, BIG)
# write output
f = open(output_file,'w')
try:
f.write(c.getNewick(with_distances=True))
except AttributeError:
if c == None:
raise RuntimeError("""input file %s did not make a UPGMA tree.
Ensure it has more than one sample present""" % (str(input_file),))
raise
f.close()
def single_file_upgma(input_file, output_file):
# read in dist matrix
f = open(input_file, 'U')
headers, data = parse_distmat(f)
f.close()
# do upgma
nodes = map(PhyloNode, headers)
BIG = 1e305
U = data.copy()
for i in range(len(U)):
U[i, i] = BIG
c = UPGMA_cluster(U, nodes, BIG)
# write output
f = open(output_file, 'w')
try:
f.write(c.getNewick(with_distances=True))
except AttributeError:
if c == None:
raise RuntimeError("""input file %s did not make a UPGMA tree.
Ensure it has more than one sample present""" % (str(input_file), ))
raise
f.close()
