def main():
parser = argparse.ArgumentParser(
description = (" Agglomerative Hierarchical Cluster Implementation "),
)
# args
parser.add_argument("--exp-file", required=True, help="Expression Matrix / TSV file")
parser.add_argument("--clust-type", default="S", choices=["S", "C", "A"], help="Type of clustering")
parser.add_argument("-k", type=int, help="Number of clusters", default=2)
opts = parser.parse_args()
(annotations, expression) = read_exp_data(opts.exp_file)
# report some stuff
log.info("Loaded expression/annotations for %i genes", len(annotations))
clusterObj = Cluster(expression, annotations)
print clusterObj.cluster(opts.clust_type, opts.k)
def testAverageTwo(self):
clusterObj = Cluster(self.expression, self.annotations)
results = read_results("./test/key/avg-2.out")
clusters = clusterObj.cluster("A",2)
self.assertEqual(results, clusters)
def testCompleteSix(self):
clusterObj = Cluster(self.expression, self.annotations)
results = read_results("./test/key/complete-6.out")
clusters = clusterObj.cluster("C",6)
self.assertEqual(results, clusters)
def testSingleSix(self):
clusterObj = Cluster(self.expression, self.annotations)
results = read_results("./test/key/single-6.out")
clusters = clusterObj.cluster("S",6)
self.assertEqual(results, clusters)