import sys
# RPy hack, make it silent
import rpy_options
rpy_options.set_options(VERBOSE=False)
import rpy
class Test(object):
methods = []
def register(cls, callable, name, desc, type_=2):
cls.methods.append((callable, name.strip(), desc.strip(), type_))
register = classmethod(register)
def __call__(self, method, *args, **kargs):
for i in self.methods:
if i[1] == method.strip():
return i[0](*args, **kargs)
raise KeyError, 'Unsupported statistic test method, %s' % method
def hyper(m1, n1, m2, n2, is_tail=False, **kargs):
""" check significance based on R language
"""
q, m, n, k = m1, m2, n2 - m2, n1
if m < q: return 0
if is_tail:
if q == 0:
"""Find enriched pathways by frequency of terms and statistical
significance of terms."""
import os, string, csv
from sets import Set
# RPy hack, make it silent
import rpy_options
rpy_options.set_options(VERBOSE=False)
import rpy
from kobas import dbutils, exception
class Dist(dict):
def __init__(self):
dict.__init__(self)
def add(self, class_, stuff):
self[class_] = stuff
def update(self, class_, iterable):
for record in iterable:
self.add(class_, record)
def size(self):
stuffs = Set()
for rec in self.values():
stuffs.update(rec)
return len(stuffs)