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#!/usr/bin/env python
"""Tests Filter, Organizer and filterfunctions, classes for filtering
"""
from cogent.util.organizer import Filter, Organizer, GroupList, regroup
from cogent.util.transform import find_any, find_no, find_all,\
keep_if_more, exclude_if_more, keep_if_more_other, exclude_if_more_other
from cogent.util.unit_test import TestCase,main
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Sandra Smit", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Production"
class Sequence(object):
"""Simple sequence class for tests."""
def __init__(self, s, info):
self.s = s
self.__dict__.update(info)
if not hasattr(self, 'Gene'):
self.Gene = None
def __contains__(self, s):
return s in self.s
def __repr__(self):
return `self.s`
def __iter__(self):
return iter(self.s)
def __nonzero__(self):
return bool(self.s)
def lower(self):
return self.s.lower()
def __cmp__(self, other):
return cmp(self.s,other.s)
class FilterTests(TestCase):
"""Tests of Filter class"""
def test_init(self):
"""Filter should init as expected"""
empty_filter = Filter('',{})
named_empty_filter = Filter('Archaea',{})
self.assertEqual(empty_filter,{})
self.assertEqual(empty_filter.Name,'')
self.assertEqual(named_empty_filter,{})
self.assertEqual(named_empty_filter.Name,'Archaea')
f = find_all('abcd')
g = keep_if_more_other('ab',7)
fil = Filter('Archaea',{'Arch':[f,g]})
assert fil['Arch'][0] is f
assert fil['Arch'][1] is g
def test_call_empty(self):
"""Empty Filter should return True when called on anything"""
f = Filter('',{})
data = ['aa','bb','cc']
self.assertEqual(f(data),True)
def test_call_full(self):
"""Filter should return True if the object satisfies all criteria"""
seq1 = Sequence('ACGU',{'Gene':'LSU'})
seq2 = Sequence('ACGUACGU',{'Gene':'SSU'})
seq3 = Sequence('ACGUN',{'Gene':'LSU'})
seq4 = Sequence('ACG',{'Gene':'LSU'})
seq5 = Sequence('ACGU',{})
seq6 = Sequence('',{})
f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\
'Gene':[find_any(['LSU'])]})
self.assertEqual(f(seq1),True)
self.assertEqual(f(seq2),False)
self.assertEqual(f(seq3),False)
self.assertEqual(f(seq4),False)
self.assertEqual(f(seq5),False)
self.assertEqual(f(seq6),False)
class GroupListTests(TestCase):
"""Tests of GroupList class"""
def test_init_empty(self):
"""Empty GroupList should init OK"""
g = GroupList([])
self.assertEqual(len(g),0)
self.assertEqual(g.Groups,[])
def test_init_full(self):
"""GroupList should init OK with data and groups"""
data = ['a','b','c']
groups = [1,2,3]
g = GroupList(data,groups)
self.assertEqual(g,data)
self.assertEqual(g.Groups,groups)
self.assertEqual(len(g),3)
class OrganizerTests(TestCase):
"""Tests of Classifier class"""
def setUp(self):
"""Define some standard Organizers for testing"""
self.Empty = Organizer([])
self.a = Filter('a',{None:[find_any('a')]})
self.b = Filter('b',{None:[find_any('b')]})
self.Ab_org = Organizer([self.a,self.b])
lsu = Filter('LSU',{None:[exclude_if_more('N',5)],\
'Gene':[find_any(['LSU'])]})
ssu = Filter('SSU',{None:[exclude_if_more('N',5)],\
'Gene':[find_any(['SSU'])]})
self.Gene_org = Organizer([lsu,ssu])
self.Ab_seq = ['aa','bb','abab','cc','']
self.seq1 = Sequence('ACGU',{'Gene':'LSU'})
self.seq2 = Sequence('ACGUACGU',{'Gene':'SSU'})
self.seq3 = Sequence('ACGUNNNNNN',{'Gene':'LSU'})
self.seq4 = Sequence('ACGUNNNNNN',{'Gene':'SSU'})
self.seq5 = Sequence('ACGU',{})
self.seq6 = Sequence('',{})
self.seq7 = Sequence('ACGU',{'Gene':'unit'})
self.Gene_seq = [self.seq1,self.seq2,self.seq3,self.seq4,\
self.seq5,self.seq6,self.seq7]
f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\
'Gene':[find_any(['LSU'])]})
self.Mult_func_org = Organizer([f])
def test_init_empty(self):
"""Empty Organizer should init correctly"""
org = self.Empty
self.assertEqual(len(org),0)
def test_init_full(self):
"""Organizer should init correctly with multiple functions"""
org = Organizer([self.a,self.b])
self.assertEqual(org[0],self.a)
self.assertEqual(org[1],self.b)
self.assertEqual(len(org),2)
def test_empty_org_empty_list(self):
"""Empty Organizer should return [] when applied to []"""
org = self.Empty
l = []
self.assertEqual(org(l),[])
def test_empty_org_full_list(self):
"""Empty organizer, applied to full list, should return the original"""
org = self.Empty
l = self.Ab_seq
obs = org(l)
self.assertEqual(obs,[l])
self.assertEqual(obs[0].Groups,[None])
def test_full_org_empty_list(self):
"""Organizer should return [] when applied to []"""
org = self.Ab_org
l = []
obs = org(l)
self.assertEqual(obs,[])
def test_full_org_full_list(self):
"""Organizer should return correct organization"""
org = self.Ab_org
l = self.Ab_seq
obs = org(l)
obs.sort()
exp = [['aa','abab'],['bb'],['cc','']]
self.assertEqual(obs,exp)
self.assertEqual(obs[0].Groups,['a'])
self.assertEqual(obs[1].Groups,['b'])
self.assertEqual(obs[2].Groups,[None])
def test_double_org_empty_list(self):
"""Organizer should return [] when applied to []"""
org = self.Gene_org
l = []
obs = org(l)
self.assertEqual(obs,[])
def test_double_org_full_list(self):
"""Organizer should handle multiple filters correctly"""
org = self.Gene_org
l = self.Gene_seq
obs = org(l)
obs.sort()
exp = [[self.seq1],[self.seq2],[self.seq3,self.seq4,\
self.seq5,self.seq6,self.seq7]]
self.assertEqual(obs,exp)
self.assertEqual(obs[0].Groups,['LSU'])
self.assertEqual(obs[1].Groups,['SSU'])
self.assertEqual(obs[2].Groups,[None])
def test_multiple_func(self):
"""Organizer should handle filter with multiple functions correctly"""
org = self.Mult_func_org
l = self.Gene_seq
obs = org(l)
obs.sort()
exp = [[self.seq1],[self.seq2,self.seq3,self.seq4,self.seq5,\
self.seq6,self.seq7]]
self.assertEqual(obs,exp)
self.assertEqual(obs[0].Groups,['valid'])
self.assertEqual(obs[1].Groups,[None])
class organizerTests(TestCase):
"""Tests for module-level functions"""
def test_regroup(self):
"""regroup: should groups with identical hierarchy-info together"""
g1 = GroupList([1,2,3],['a'])
g2 = GroupList([4,5,6],['b'])
g3 = GroupList([7,7,7],['a','b'])
g4 = GroupList([8,8,8],['a'])
all = [g1, g2, g3, g4]
self.assertEqualItems(regroup(all), [[1,2,3,8,8,8],[7,7,7],[4,5,6]])
if __name__ == "__main__":
main()
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