def diversity_ana(metric,subsample,ids,**kwargs):
if metric == 'faith_pd':
each = alpha_diversity('faith_pd', subsample, ids=ids,
otu_ids=kwargs['otu_ids'], tree=kwargs['tree'])
elif metric == 'shannon':
each = alpha_diversity('shannon', subsample, ids=ids)
elif metric == 'observed_otus':
each = alpha_diversity('observed_otus', subsample, ids=ids)
else:
try:
each = alpha_diversity(metric, subsample, ids=ids)
except:
print 'Metric you can use is listed below: \n' + '\n'.join(get_alpha_diversity_metrics())
exit()
return each
def test_get_alpha_diversity_metrics_sorted(self):
m = get_alpha_diversity_metrics()
n = sorted(list(m))
self.assertEqual(m, n)
def test_get_alpha_diversity_metrics(self):
m = get_alpha_diversity_metrics()
# basic sanity checks
self.assertTrue('faith_pd' in m)
self.assertTrue('chao1' in m)
def test_get_alpha_diversity_metrics_sorted(self):
m = get_alpha_diversity_metrics()
n = sorted(list(m))
self.assertEqual(m, n)
def test_get_alpha_diversity_metrics(self):
m = get_alpha_diversity_metrics()
# basic sanity checks
self.assertTrue('faith_pd' in m)
self.assertTrue('chao1' in m)
default='class')
parser.add_argument('--list_metric', action='store_true',
help="List all metric name you could use.")
parser.add_argument('--output_fig',
help="If you need to remodify figure, you can assign file path, we will pickle it into file.")
args = parser.parse_args()
threads = args.thread
tree_file = args.tree
Otu_table = args.input
metadata = args.metadata
output_dir = args.output
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if args.list_metric:
print 'Metric you can use is listed below: \n' + '\n'.join(get_alpha_diversity_metrics())
exit()
metric = args.metric
if ',' in metric:
metric = metric.split(',')
else:
metric = [metric]
step = args.step
repeat = args.repeat
col_need = args.cols
ori_otu = read_data(Otu_table)
if metadata:
sample_info = read_data(metadata)
if tree_file:
tree = TreeNode.read(tree_file, format='newick')
parser.add_argument('--list_metric', action='store_true',
help="List all metric name you could use.")
parser.add_argument('--output_fig',
help="If you need to remodify figure, you can assign file path, we will pickle it into file.")
args = parser.parse_args()
threads = args.thread
tree_file = args.tree
Otu_table = args.input
metadata = args.metadata
output_dir = args.output
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if args.list_metric:
print('Metric you can use is listed below: \n' +
'\n'.join(get_alpha_diversity_metrics()))
exit()
metric = args.metric
if ',' in metric:
metric = metric.split(',')
else:
metric = [metric]
step = args.step
repeat = args.repeat
col_need = args.cols
ori_otu = read_data(Otu_table)
if metadata:
sample_info = read_data(metadata)
if tree_file:
tree = TreeNode.read(tree_file, format='newick')
