def analyze_consensus_clusters():
logging.debug('parse the gene names')
data_filename = sys.argv[1]
names = get_gene_names(data_filename)
logging.debug('get clusters from the first tree')
tree_filename = sys.argv[2]
root = get_tree(tree_filename)
root = treebuilder.center_and_sort_tree(root)
first_clusters = treebuilder.get_clusters(root)
logging.debug('get clusters from the second tree')
tree_filename = sys.argv[3]
root = get_tree(tree_filename)
root = treebuilder.center_and_sort_tree(root)
second_clusters = treebuilder.get_clusters(root)
logging.debug('get consensus clusters')
consensus = set(frozenset(c) for c in first_clusters) & set(frozenset(c) for c in second_clusters)
logging.debug('show the corresponding genes')
length_cluster_pairs = list(sorted((len(c), list(c)) for c in consensus))
for l, c in length_cluster_pairs:
#print len(c)
print ', '.join(names[x] for x in c)
def analyze_clusters():
"""
First arg is data file, second arg is newick file.
"""
logging.debug('parse the gene names')
data_filename = sys.argv[1]
names = get_gene_names(data_filename)
logging.debug('parse the tree')
tree_filename = sys.argv[2]
root = get_tree(tree_filename)
logging.debug('center and sort the tree')
root = treebuilder.center_and_sort_tree(root)
logging.debug('get the clusters')
clusters = treebuilder.get_clusters(root)
logging.debug('show the corresponding genes')
length_cluster_pairs = list(sorted((len(c), list(c)) for c in clusters))
for l, c in length_cluster_pairs:
#print len(c)
print ', '.join(names[x] for x in c)
