#!/usr/bin/env python """Unit tests for Mage format writer. """ from __future__ import division from numpy import array from copy import deepcopy from cogent.util.unit_test import TestCase, main from cogent.format.mage import MagePoint, MageList, MageGroup, MageHeader, \ Kinemage, MagePointFromBaseFreqs from cogent.core.usage import BaseUsage from cogent.util.misc import Delegator __author__ = "Rob Knight" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Sandra Smit", "Gavin Huttley", "Rob Knight"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "Gavin Huttley" __email__ = "gavin.huttley@anu.edu.au" __status__ = "Production" class MagePointTests(TestCase): """Tests of the MagePoint class, holding information about points.""" def test_init_empty(self): """MagePoint should init correctly with no data""" m = MagePoint() self.assertEqual(str(m), ' '.join(map(str,[0,0,0]))) def test_init(self): """MagePoint should init correctly with normal cases""" #label and coords m = MagePoint([0.200,0.000,0.800], '0.800') self.assertEqual(str(m), '{0.800} ' + \ ' '.join(map(str, ([0.200,0.000,0.800])))) #coords only m = MagePoint([0.200,0.000,0.800]) self.assertEqual(str(m), ' '.join(map(str, ([0.200,0.000,0.800])))) #label only m = MagePoint(Label='abc') self.assertEqual(str(m), '{abc} '+' '.join(map(str,[0,0,0]))) #all fields occupied m = MagePoint(Label='abc', Coordinates=[3, 6, 1.5], Radius=0.5, \ Width=2, State='P', Color='green') self.assertEqual(str(m), \ '{abc} P green width2 r=0.5 3 6 1.5') def test_cmp(self): """MagePoint cmp should compare all fields""" self.assertEqual(MagePoint([0,0,0]), MagePoint([0,0,0])) self.assertNotEqual(MagePoint([0,0,0]), MagePoint([0,0,0], Color='red')) def test_get_coord(self): """MagePoint _get_coord should return coordinate that is asked for""" m = MagePoint([0,1,2]) self.assertEqual(m.X,m.Coordinates[0]) self.assertEqual(m.Y,m.Coordinates[1]) self.assertEqual(m.Z,m.Coordinates[2]) m = MagePoint() self.assertEqual(m.X,m.Coordinates[0]) self.assertEqual(m.Y,m.Coordinates[1]) self.assertEqual(m.Z,m.Coordinates[2]) def test_set_coord(self): """MagePoint _get_coord should return coordinate that is asked for""" m = MagePoint([0,1,2]) m.X, m.Y, m.Z = 2,3,4 self.assertEqual(m.Coordinates,[2,3,4]) m = MagePoint() m.X, m.Y, m.Z = 5,4,3 self.assertEqual(m.Coordinates,[5,4,3]) m = MagePoint() m.X = 5 self.assertEqual(m.Coordinates,[5,0,0]) def test_toCartesian(self): """MagePoint toCartesian() should transform coordinates correctly""" m = MagePoint([.1,.2,.3]) self.assertEqual(m.toCartesian().Coordinates,[.6,.7,.5]) m = MagePoint() self.assertEqual(m.toCartesian().Coordinates,[1,1,1]) m = MagePoint([.25,.25,.25],Color='red',Label='label',State='L') self.assertEqual(m.toCartesian().Coordinates,[.5,.5,.5]) self.assertEqual(m.toCartesian().Color,m.Color) self.assertEqual(m.toCartesian().Label,m.Label) self.assertEqual(m.toCartesian().State,m.State) m = MagePoint([1/3.0,1/3.0,0]) self.assertFloatEqual(m.toCartesian().Coordinates, [2/3.0,1/3.0,2/3.0]) m = MagePoint([1/3.0,1/3.0,1/3.0]) self.assertFloatEqual(m.toCartesian().Coordinates, [1/3.0,1/3.0,1/3.0]) m = MagePoint([3,4,5]) self.assertRaises(ValueError,m.toCartesian) def test_fromCartesian(self): """MagePoint fromCartesian should transform coordinates correctly""" mp = MagePoint([2/3.0,1/3.0,2/3.0]) self.assertFloatEqual(mp.fromCartesian().Coordinates,[1/3.0,1/3.0,0]) points = [MagePoint([.1,.2,.3]),MagePoint([.25,.25,.25],Color='red', Label='label',State='L'),MagePoint([1/3,1/3,0]), MagePoint([0,0,0]),MagePoint([1/7,2/7,3/7])] for m in points: b = m.toCartesian().fromCartesian() self.assertFloatEqual(m.Coordinates,b.Coordinates) self.assertEqual(m.Color,b.Color) self.assertEqual(m.Label,b.Label) self.assertEqual(m.State,b.State) #even after multiple iterations? mutant = deepcopy(m) for x in range(10): mutant = mutant.toCartesian().fromCartesian() self.assertFloatEqual(m.Coordinates,mutant.Coordinates) class freqs_label(dict): """dict with Label and Id, for testing MagePointFromBaseFreqs""" def __init__(self, Label, Id, freqs): self.Label = Label self.Id = Id self.update(freqs) class freqs_display(dict): """dict with display properties, for testing MagePointFromBaseFreqs""" def __init__(self, Color, Radius, Id, freqs): self.Color = Color self.Radius = Radius self.Id = Id self.update(freqs) class MagePointFromBaseFreqsTests(TestCase): """Tests of the MagePointFromBaseFreqs factory function.""" def setUp(self): """Define a few standard frequencies""" self.empty = freqs_label(None, None, {}) self.dna = freqs_label('dna', None, {'A':4, 'T':1, 'G':2, 'C':3}) self.rna = freqs_label(None, 'rna', {'U':2, 'A':1, 'G':2}) self.display = freqs_display('green', '0.25', 'xxx', {'A':2}) def test_MagePointFromBaseFreqs(self): """MagePoint should fill itself from base freqs correctly""" e = MagePointFromBaseFreqs(self.empty) self.assertEqual(str(e), '0.0 0.0 0.0') dna = MagePointFromBaseFreqs(self.dna) self.assertEqual(str(dna), '{dna} 0.4 0.3 0.2') rna = MagePointFromBaseFreqs(self.rna) self.assertEqual(str(rna), '{rna} 0.2 0.0 0.4') display = MagePointFromBaseFreqs(self.display) self.assertEqual(str(display), \ '{xxx} green r=0.25 1.0 0.0 0.0') def test_MagePointFromBaseFreqs_usage(self): """MagePoint should init correctly from base freqs""" class fake_seq(str, Delegator): def __new__(cls, data, *args): return str.__new__(cls, data) def __init__(self, data, *args): Delegator.__init__(self, *args) self.__dict__['Info'] = self._handler str.__init__(data) class has_species(object): def __init__(self, sp): self.Species = sp s = fake_seq('AAAAACCCTG', has_species('Homo sapiens')) b = BaseUsage(s) p = MagePointFromBaseFreqs(b) self.assertEqual(str(p), '{Homo sapiens} 0.5 0.3 0.1') def test_MagePointFromBaseFreqs_functions(self): """MagePointFromBaseFreqs should apply functions correctly""" def set_color(x): if x.Label == 'dna': return 'green' else: return 'blue' def set_radius(x): if x.Label == 'dna': return 0.25 else: return 0.5 def set_label(x): if x.Id is not None: return 'xxx' else: return 'yyy' self.assertEqual(str(MagePointFromBaseFreqs(self.dna, get_label=set_label)), '{yyy} 0.4 0.3 0.2') self.assertEqual(str(MagePointFromBaseFreqs(self.rna, get_label=set_label)), '{xxx} 0.2 0.0 0.4') self.assertEqual(str(MagePointFromBaseFreqs(self.dna, get_radius=set_radius)), '{dna} r=0.25 0.4 0.3 0.2') self.assertEqual(str(MagePointFromBaseFreqs(self.rna, get_radius=set_radius)), '{rna} r=0.5 0.2 0.0 0.4') self.assertEqual(str(MagePointFromBaseFreqs(self.dna, get_color=set_color)), '{dna} green 0.4 0.3 0.2') self.assertEqual(str(MagePointFromBaseFreqs(self.rna, get_color=set_color)), '{rna} blue 0.2 0.0 0.4') self.assertEqual(str(MagePointFromBaseFreqs(self.rna, get_label=set_label, get_radius=set_radius,get_color=set_color)), '{xxx} blue r=0.5 0.2 0.0 0.4') class MageListTests(TestCase): """Tests of the MageList class, holding a collection of points.""" def setUp(self): """Define a few standard points and lists of points.""" self.null = MagePoint([0,0,0]) self.label = MagePoint([1, 1, 1], 'test') self.properties = MagePoint(Width=1, Label='point', State='L',\ Color='blue', Coordinates=[2.0,4.0,6.0]) self.radius1 = MagePoint([2,2,2],Radius=.1) self.radius2 = MagePoint([3,3,3],Radius=.5) self.first_list = [self.null, self.properties] self.empty_list = [] self.minimal_list = [self.null] self.single_list = [self.label] self.multi_list = [self.properties] * 10 self.radii = [self.radius1,self.radius2] def test_init_empty(self): """MageList should init correctly with no data""" m = MageList() self.assertEqual(str(m), "@dotlist") m = MageList(self.empty_list) self.assertEqual(str(m), "@dotlist") def test_init(self): """MageList should init correctly with data""" m = MageList(self.minimal_list) self.assertEqual(str(m), "@dotlist\n" + str(self.null)) m = MageList(self.multi_list,'x',Off=True,Color='green',NoButton=True) self.assertEqual(str(m), "@dotlist {x} off nobutton color=green\n" + \ '\n'.join(10 * [str(self.properties)])) m = MageList(self.first_list,NoButton=True,Color='red', \ Style='vector', Radius=0.03, Width=3, Label='test') self.assertEqual(str(m), "@vectorlist {test} nobutton color=red " + \ "radius=0.03 width=3\n" + str(self.null) + '\n' + str(self.properties)) def test_toArray_radii(self): """MageList toArray should return the correct array""" m = MageList(self.empty_list) self.assertEqual(m.toArray(),array(())) m = MageList(self.first_list,Radius=.3) self.assertEqual(m.toArray(),array([[0,0,0,0.3],[2.0,4.0,6.0,0.3]])) m = MageList(self.radii) self.assertEqual(m.toArray(), array([[2,2,2,.1],[3,3,3,.5]])) m = MageList(self.radii,Radius=.4) self.assertEqual(m.toArray(), array([[2,2,2,.1],[3,3,3,.5]])) m = MageList(self.single_list) #radius = None self.assertRaises(ValueError,m.toArray) def test_toArray_coords_only(self): """MageList toArray should return the correct array""" m = MageList(self.empty_list) self.assertEqual(m.toArray(include_radius=False),array(())) m = MageList(self.first_list,Radius=.3) self.assertEqual(m.toArray(include_radius=False), array([[0,0,0],[2.0,4.0,6.0]])) m = MageList(self.radii) self.assertEqual(m.toArray(include_radius=False), array([[2,2,2],[3,3,3]])) m = MageList(self.radii,Radius=.4) self.assertEqual(m.toArray(include_radius=False), array([[2,2,2],[3,3,3]])) m = MageList(self.single_list) #radius = None self.assertEqual(m.toArray(include_radius=False),array([[1,1,1]])) def test_iterPoints(self): """MageList iterPoints should yield all points in self""" m = MageList(self.single_list) for point in m.iterPoints(): assert isinstance(point,MagePoint) self.assertEqual(len(list(m.iterPoints())),1) m = MageList(self.multi_list) for point in m.iterPoints(): assert isinstance(point,MagePoint) self.assertEqual(len(list(m.iterPoints())),10) def test_toCartesian(self): """MageList toCartesian should return new list""" m = MageList([self.null],Color='green') res = m.toCartesian() self.assertEqual(len(m), len(res)) self.assertEqual(m.Color,res.Color) self.assertEqual(res[0].Coordinates,[1,1,1]) m.Color='red' self.assertEqual(res.Color,'green') m = MageList([self.properties]) self.assertRaises(ValueError,m.toCartesian) def test_fromCartesian(self): """MageList fromCartesian() should return new list with ACG coordinates """ point = MagePoint([.1,.2,.3]) m = MageList([point]*5,Color='green') res = m.toCartesian().fromCartesian() self.assertEqual(str(m),str(res)) class MageGroupTests(TestCase): """Test cases for the MageGroup class.""" def setUp(self): """Define some standard lists and groups.""" self.p1 = MagePoint([0, 1, 0], Color='green', Label='x') self.p0 = MagePoint([0,0,0]) self.min_list = MageList([self.p0]*2,'y') self.max_list = MageList([self.p1]*5,'z',Color='blue',Off=True, \ Style='ball') self.min_group = MageGroup([self.min_list], Label="min_group") self.max_group = MageGroup([self.min_list, self.max_list], Color='red', Label="max_group", Style='dot') self.nested = MageGroup([self.min_group, self.max_group], Label='nest', Color='orange', Radius=0.3, Style='vector') self.empty = MageGroup(Label='empty',Color='orange', NoButton=True, Style='vector',RecessiveOn=False) def test_init(self): """Nested MageGroups should set subgroup and cascades correctly.""" exp_lines = [ '@group {nest} recessiveon', '@subgroup {min_group} recessiveon', '@vectorlist {y} color=orange radius=0.3', str(self.p0), str(self.p0), '@subgroup {max_group} recessiveon', '@dotlist {y} color=red radius=0.3', str(self.p0), str(self.p0), '@balllist {z} off color=blue radius=0.3', str(self.p1), str(self.p1), str(self.p1), str(self.p1), str(self.p1), ] s = str(self.nested).split('\n') self.assertEqual(str(self.nested), '\n'.join(exp_lines)) #check that resetting the cascaded values works OK nested = self.nested str(nested) self.assertEqual(nested,self.nested) self.assertEqual(nested[0][0].Color,None) def test_str(self): """MageGroup str should print correctly""" m = self.empty self.assertEqual(str(self.empty),'@group {empty} nobutton') m = MageGroup(Label='label',Clone='clone_name',Off=True) self.assertEqual(str(m), '@group {label} off recessiveon clone={clone_name}') m = MageGroup() self.assertEqual(str(m),'@group recessiveon') def test_iterGroups(self): """MageGroup iterGroups should behave as expected""" groups = list(self.nested.iterGroups()) self.assertEqual(groups[0],self.min_group) self.assertEqual(groups[1],self.max_group) self.assertEqual(len(groups),2) def test_iterLists(self): """MageGroup iterLists should behave as expected""" lists = list(self.nested.iterLists()) self.assertEqual(len(lists),3) self.assertEqual(lists[0],self.min_list) self.assertEqual(lists[1],self.min_list) self.assertEqual(lists[2],self.max_list) def test_iterGroupsAndLists(self): """MageGroup iterGroupsAndLists should behave as expected""" all = list(self.nested.iterGroupsAndLists()) self.assertEqual(len(all),5) self.assertEqual(all[0],self.min_group) self.assertEqual(all[4],self.max_list) def test_iterPoints(self): """MageGroup iterPoints should behave as expected""" points = list(self.nested.iterPoints()) self.assertEqual(len(points),9) self.assertEqual(points[1],self.p0) self.assertEqual(points[6],self.p1) def test_toCartesian(self): """MageGroup toCartesian should return a new MageGroup""" m = self.nested res = m.toCartesian() self.assertEqual(len(m),len(res)) self.assertEqual(m.RecessiveOn,res.RecessiveOn) self.assertEqual(m[1][1].Color, res[1][1].Color) self.assertEqual(res[1][1][1].Coordinates,[1,0,0]) def test_fromCartesian(self): """MageGroup fromCartesian should return a new MageGroup""" point = MagePoint([.1,.2,.3]) l = MageList([point]*5,Color='red') m = MageGroup([l],Radius=0.02,Subgroup=True) mg = MageGroup([m]) res = mg.toCartesian().fromCartesian() self.assertEqual(str(mg),str(res)) class MageHeaderTests(TestCase): """Tests of the MageHeader class. For now, MageHeader does nothing, so just verify that it gets the string. """ def test_init(self): """MageHeader should keep the string it was initialized with.""" m = MageHeader('@perspective') self.assertEqual(str(m), '@perspective') class KinemageTests(TestCase): """Tests of the overall Kinemage class.""" def setUp(self): self.point = MagePoint([0,0,0],'x') self.ml = MageList([self.point], Label='y',Color='green') self.mg1 = MageGroup([self.ml],Label='z') self.mg2 = MageGroup([self.ml,self.ml],Label='b') self.kin = Kinemage(1) self.kin.Groups = [self.mg1,self.mg2] def test_init_empty(self): """Kinemage empty init should work, but refuse to print""" k = Kinemage() self.assertEqual(k.Count, None) self.assertRaises(ValueError, k.__str__) def test_init(self): """Kinemage should init with any of its usual fields""" k = Kinemage(1) self.assertEqual(str(k), '@kinemage 1') k.Header = '@perspective' self.assertEqual(str(k), '@kinemage 1\n@perspective') k.Count = 2 self.assertEqual(str(k), '@kinemage 2\n@perspective') k.Header = '' k.Caption = 'test caption' self.assertEqual(str(k), '@kinemage 2\n@caption\ntest caption') k.Caption = None k.Text = 'some text' self.assertEqual(str(k), '@kinemage 2\n@text\nsome text') k.Groups = [self.mg1] k.Header = '@test_header' k.Caption = 'This is\nThe caption' k.Text = 'some text here' self.assertEqual(str(k), '@kinemage 2\n@test_header\n@text\n' +\ 'some text here\n' + \ '@caption\nThis is\nThe caption\n@group {z} recessiveon\n' + \ '@dotlist {y} color=green\n{x} 0 0 0') def test_iterGroups(self): """Kinemage iterGroups should behave as expected""" k = self.kin groups = list(k.iterGroups()) self.assertEqual(len(groups),2) self.assertEqual(groups[0],self.mg1) self.assertEqual(groups[1],self.mg2) def test_iterLists(self): """Kinemage iterLists should behave as expected""" k = self.kin lists = list(k.iterLists()) self.assertEqual(len(lists),3) self.assertEqual(lists[0],self.ml) def test_iterPoints(self): """Kinemage iterPoints should behave as expected""" k = self.kin points = list(k.iterPoints()) self.assertEqual(len(points),3) self.assertEqual(points[0],self.point) def test_iterGroupAndLists(self): """Kinemage iterGroupsAndLists should behave as expected""" all = list(self.kin.iterGroupsAndLists()) self.assertEqual(len(all),5) self.assertEqual(all[0],self.mg1) self.assertEqual(all[4],self.ml) def test_toCartesian(self): """Kinemage toCartesian should return new Kinemage with UC,UG,UA coords """ k = self.kin res = k.toCartesian() self.assertEqual(len(k.Groups),len(res.Groups)) self.assertEqual(k.Text,res.Text) self.assertEqual(k.Groups[1].RecessiveOn,res.Groups[1].RecessiveOn) self.assertEqual(res.Groups[0][0][0].Coordinates,[1,1,1]) def test_fromCartesian(self): """Kinemage fromCartesian should return Kinemage with A,C,G(,U) coords """ point = MagePoint([.1,.2,.3]) l = MageList([point]*5,Color='red') m1 = MageGroup([l],Radius=0.02,Subgroup=True) m2 = MageGroup([l],Radius=0.02) mg = MageGroup([m1]) k = Kinemage(Count=1,Groups=[mg,m2]) res = k.toCartesian().fromCartesian() self.assertEqual(str(k),str(res)) if __name__ == '__main__': main()