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()