#!/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()