#!/usr/bin/env python
#file cogent_tests/motif/test_util.py
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
MotifResults, MotifFormatter, html_color_to_rgb
from cogent.core.moltype import ASCII
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Production"
class LocationTests(TestCase):
"""Tests of Location class for holding module location.
"""
def setUp(self):
"""Setup for Location tests."""
self.location_no_end = Location('seq1',1)
self.locations = [
Location('seq1',1,5),
Location('seq2',3,54),
Location('seq1',5,3),
Location('seq1',2,3),
Location('seq2',54,2),
Location('seq0',1,3),
]
self.locations_sorted = [
Location('seq0',1,3),
Location('seq1',1,5),
Location('seq1',5,3),
Location('seq1',2,3),
Location('seq2',3,54),
Location('seq2',54,2),
]
def test_init_no_end(self):
"""__init__ should properly initialize Location object"""
self.assertEqual(self.location_no_end.SeqId, 'seq1')
self.assertEqual(self.location_no_end.Start, 1)
self.assertEqual(self.location_no_end.End, 2)
def test_init_complete(self):
"""__init__ should properly initialize Location object"""
self.assertEqual(self.locations[0].SeqId, 'seq1')
self.assertEqual(self.locations[0].Start, 1)
self.assertEqual(self.locations[0].End, 5)
def test_cmp(self):
"""Location object should sort properly with __cmp__ overwritten."""
self.locations.sort()
self.assertEqual(self.locations, self.locations_sorted)
class ModuleInstanceTests(TestCase):
"""Tests for ModuleInstance class."""
def setUp(self):
"""Setup function for ModuleInstance tests."""
self.sequences = [
'accucua',
'caucguu',
'accucua',
'cgacucg',
'cgaucag',
'cuguacc',
'cgcauca',
]
self.locations = [
Location('seq0',1,3),
Location('seq1',2,3),
Location('seq1',1,5),
Location('seq1',5,3),
Location('seq2',3,54),
Location('seq2',54,2),
Location('seq3',4,0),
]
self.Pvalues = [
.1,
.002,
.0000000003,
.6,
.0094,
.6,
.00201,
]
self.Evalues = [
.006,
.02,
.9,
.0200000001,
.09,
.0000003,
.900001,
]
self.modules_no_e = []
for i in xrange(7):
self.modules_no_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i]))
self.modules_p_and_e = []
for i in xrange(7):
self.modules_p_and_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i],
self.Evalues[i]))
self.modules_no_e_sorted = [
ModuleInstance(self.sequences[2],self.locations[2],self.Pvalues[2]),
ModuleInstance(self.sequences[1],self.locations[1],self.Pvalues[1]),
ModuleInstance(self.sequences[6],self.locations[6],self.Pvalues[6]),
ModuleInstance(self.sequences[4],self.locations[4],self.Pvalues[4]),
ModuleInstance(self.sequences[0],self.locations[0],self.Pvalues[0]),
ModuleInstance(self.sequences[3],self.locations[3],self.Pvalues[3]),
ModuleInstance(self.sequences[5],self.locations[5],self.Pvalues[5]),
]
self.modules_p_and_e_sorted = [
ModuleInstance(self.sequences[2],self.locations[2],self.Pvalues[2]),
ModuleInstance(self.sequences[1],self.locations[1],self.Pvalues[1]),
ModuleInstance(self.sequences[6],self.locations[6],self.Pvalues[6]),
ModuleInstance(self.sequences[4],self.locations[4],self.Pvalues[4]),
ModuleInstance(self.sequences[0],self.locations[0],self.Pvalues[0]),
ModuleInstance(self.sequences[5],self.locations[5],self.Pvalues[5]),
ModuleInstance(self.sequences[3],self.locations[3],self.Pvalues[3]),
]
def test_init_no_p_e_values(self):
"""Init should properly initialize ModuleInstance objects."""
module1 = ModuleInstance(self.sequences[0], self.locations[0])
module2 = ModuleInstance(self.sequences[1], self.locations[1])
self.assertEqual(module1.Sequence, 'accucua')
self.assertEqual(module1.Location.SeqId, 'seq0')
self.assertEqual(module2.Sequence, 'caucguu')
self.assertEqual(module2.Location.SeqId, 'seq1')
def test_init_no_e_values(self):
"""Init should properly initialize ModuleInstance objects."""
self.modules_no_e.sort()
self.assertEqual(self.modules_no_e, self.modules_no_e_sorted)
def test_len(self):
"""len() should return correct length of the ModuleInstance sequence."""
for module in self.modules_no_e:
self.assertEqual(len(module), 7)
def test_str(self):
"""str() should return the correct string for each ModuleInstance."""
for module, seq in zip(self.modules_no_e, self.sequences):
self.assertEqual(str(module), seq)
def test_cmp(self):
"""ModuleInstances should sort properly with __cmp__ overwritten."""
self.modules_no_e.sort()
self.modules_p_and_e.sort()
self.assertEqual(map(str,self.modules_no_e),
map(str,self.modules_no_e_sorted))
self.assertEqual(map(str,self.modules_p_and_e),
map(str,self.modules_p_and_e_sorted))
class ModuleTests(TestCase):
"""Tests for Module class."""
def setUp(self):
"""SetUp for Module class tests."""
self.sequences = [
'accucua',
'caucguu',
'accucua',
'cgacucg',
'cgaucag',
'cuguacc',
'cgcauca',
]
self.locations = [
Location('seq0',1,3),
Location('seq1',2,3),
Location('seq1',1,5),
Location('seq1',5,3),
Location('seq2',3,54),
Location('seq2',54,2),
Location('seq3',4,0),
]
self.Pvalues = [
.1,
.002,
.0000000003,
.6,
.0094,
.6,
.00201,
]
self.Evalues = [
.006,
.02,
.9,
.0200000001,
.09,
.0000003,
.900001,
]
self.modules_no_e = []
for i in xrange(7):
self.modules_no_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i]))
self.modules_p_and_e = []
for i in xrange(7):
self.modules_p_and_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i],
self.Evalues[i]))
self.module_no_template = Module(
{
(self.modules_no_e[0].Location.SeqId,
self.modules_no_e[0].Location.Start):self.modules_no_e[0],
(self.modules_no_e[1].Location.SeqId,
self.modules_no_e[1].Location.Start):self.modules_no_e[1],
(self.modules_no_e[2].Location.SeqId,
self.modules_no_e[2].Location.Start):self.modules_no_e[2],
(self.modules_no_e[3].Location.SeqId,
self.modules_no_e[3].Location.Start):self.modules_no_e[3],
(self.modules_no_e[4].Location.SeqId,
self.modules_no_e[4].Location.Start):self.modules_no_e[4],
(self.modules_no_e[5].Location.SeqId,
self.modules_no_e[5].Location.Start):self.modules_no_e[5],
(self.modules_no_e[6].Location.SeqId,
self.modules_no_e[6].Location.Start):self.modules_no_e[6],
}
)
self.module_with_template = Module(
{
(self.modules_no_e[0].Location.SeqId,
self.modules_no_e[0].Location.Start):self.modules_no_e[0],
(self.modules_no_e[1].Location.SeqId,
self.modules_no_e[1].Location.Start):self.modules_no_e[1],
(self.modules_no_e[2].Location.SeqId,
self.modules_no_e[2].Location.Start):self.modules_no_e[2],
(self.modules_no_e[3].Location.SeqId,
self.modules_no_e[3].Location.Start):self.modules_no_e[3],
(self.modules_no_e[4].Location.SeqId,
self.modules_no_e[4].Location.Start):self.modules_no_e[4],
(self.modules_no_e[5].Location.SeqId,
self.modules_no_e[5].Location.Start):self.modules_no_e[5],
(self.modules_no_e[6].Location.SeqId,
self.modules_no_e[6].Location.Start):self.modules_no_e[6],
},
Template = 'accgucg'
)
def test_init(self):
"""Init should properly initialize Module object."""
module = Module(data={(self.modules_no_e[0].Location.SeqId,
self.modules_no_e[0].Location.Start): \
self.modules_no_e[0]})
self.assertEqual(module.Template, None)
self.assertEqual(module.Alphabet, ASCII.Alphabet)
self.assertEqual(module.Pvalue, None)
self.assertEqual(module.Evalue, None)
self.assertEqual(module.keys(),[('seq0',1)])
self.assertEqual(module.values(),[ModuleInstance(self.sequences[0],
self.locations[0],
self.Pvalues[0])])
def test_cmp(self):
"""Module objects should sort properly with __cmp__ overwritten."""
pvals_sorted = [3e-010, 0.002,
0.0020100000000000001,
0.0094000000000000004,
0.10000000000000001,
0.59999999999999998,
0.59999999999999998]
evals_sorted = [.9,
.02,
.900001,
.09,
.006,
.0000003,
.0200000001,
]
modules = []
for instance, pvalue, evalue in zip(self.modules_no_e,
self.Pvalues,
self.Evalues):
modules.append(Module({(instance.Location.SeqId,
instance.Location.Start):instance},
Pvalue=pvalue,
Evalue=evalue))
modules.sort()
for ans, p, e in zip(modules, pvals_sorted, evals_sorted):
self.assertEqual(ans.Pvalue, p)
self.assertEqual(ans.Evalue, e)
def test_LocationDict(self):
"""LocationDict should return correct dictionary of locations."""
location_dict_ans = {
'seq0':[1],
'seq1':[1,2,3],
'seq2':[2,3],
'seq3':[0],
}
location_dict = self.module_no_template.LocationDict
self.assertEqual(location_dict,location_dict_ans)
class MotifTests(TestCase):
"""Tests for Motif class."""
def test_init(self):
"""Init should properly initialize Motif object."""
module = Module({
('a',3): ModuleInstance('guc', Location('a',3,5)),
('b',3): ModuleInstance('guc', Location('b',3,5)),
('c',8): ModuleInstance('guc', Location('c',8,10)),
})
m = Motif(module)
self.assertEqual(m.Modules,[module])
self.assertEqual(m.Info,None)
class MotifResultsTests(TestCase):
"""Tests for MotifResults class."""
def test_init(self):
"""Init should properly initialize MotifResults object."""
module = Module({
('a',3): ModuleInstance('guc', Location('a',3,5)),
('b',3): ModuleInstance('guc', Location('b',3,5)),
('c',8): ModuleInstance('guc', Location('c',8,10)),
})
motif = Motif([module])
results = {'key1':'value1','key2':'value2'}
parameters = {'parameter1':1,'parameter2':2}
mr = MotifResults([module],[motif],results,parameters)
self.assertEqual(mr.Modules,[module])
self.assertEqual(mr.Motifs,[motif])
self.assertEqual(mr.Results,results)
self.assertEqual(mr.parameter1,1)
self.assertEqual(mr.parameter2,2)
class UtilTests(TestCase):
"""Tests for utility functions."""
def test_html_color_to_rgb(self):
"""Tests for html_to_color_rgb."""
html_colors = ['#FF0000','#00FF00','#0000FF','545454']
rgb_colors = [(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0),\
(0.32941176470588235,0.32941176470588235,0.32941176470588235)]
for html, rgb in zip(html_colors, rgb_colors):
self.assertEqual(html_color_to_rgb(html),rgb)
def test_make_remap_dict(self):
"""Tests for make_remap_dict."""
pass
class MotifFormatterTests(TestCase):
"""Tests for MotifFormatter class."""
def setUp(self):
"""SetUp for MotifFormatter class tests."""
self.sequences = [
'accucua',
'caucguu',
'accucua',
'cgacucg',
'cgaucag',
'cuguacc',
'cgcauca',
]
self.locations = [
Location('seq0',1,3),
Location('seq1',2,3),
Location('seq1',1,5),
Location('seq1',5,3),
Location('seq2',3,54),
Location('seq2',54,2),
Location('seq3',4,0),
]
self.Pvalues = [
.1,
.002,
.0000000003,
.6,
.0094,
.6,
.00201,
]
self.Evalues = [
.006,
.02,
.9,
.0200000001,
.09,
.0000003,
.900001,
]
self.modules_no_e = []
for i in xrange(7):
self.modules_no_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i]))
self.module_with_template = Module(
{
(self.modules_no_e[0].Location.SeqId,
self.modules_no_e[0].Location.Start):self.modules_no_e[0],
(self.modules_no_e[1].Location.SeqId,
self.modules_no_e[1].Location.Start):self.modules_no_e[1],
(self.modules_no_e[2].Location.SeqId,
self.modules_no_e[2].Location.Start):self.modules_no_e[2],
(self.modules_no_e[3].Location.SeqId,
self.modules_no_e[3].Location.Start):self.modules_no_e[3],
(self.modules_no_e[4].Location.SeqId,
self.modules_no_e[4].Location.Start):self.modules_no_e[4],
(self.modules_no_e[5].Location.SeqId,
self.modules_no_e[5].Location.Start):self.modules_no_e[5],
(self.modules_no_e[6].Location.SeqId,
self.modules_no_e[6].Location.Start):self.modules_no_e[6],
},
Template = 'accgucg', ID='1'
)
self.modules_with_ids =\
[Module({
('a',3): ModuleInstance('guc', Location('a',3,5)),
('b',3): ModuleInstance('guc', Location('b',3,5)),
('c',8): ModuleInstance('guc', Location('c',8,10)),
},ID='1'),
Module({
('a',7): ModuleInstance('cca', Location('a',7,9)),
('b',7): ModuleInstance('cca', Location('b',7,9)),
('c',11): ModuleInstance('cca',Location('c',11,13)),
},ID='2'),
Module({
('a',10): ModuleInstance('gca',Location('a',10,12)),
('b',10): ModuleInstance('gca',Location('b',10,12)),
('c',14): ModuleInstance('gca',Location('c',14,12)),
},ID='3'),
Module({
('a',13): ModuleInstance('ggg',Location('a',13,15)),
('b',13): ModuleInstance('ggg',Location('b',13,15)),
('c',18): ModuleInstance('ggg',Location('c',18,20)),
},ID='4'),
]
self.motifs_with_ids = map(Motif,self.modules_with_ids)
self.motif_results = MotifResults(Modules=self.modules_with_ids,\
Motifs=self.motifs_with_ids)
self.color_map = {'1':"""background-color: #0000FF; ; font-family: 'Courier New', Courier""",
'2':"""background-color: #FFFF00; ; font-family: 'Courier New', Courier""",
'3':"""background-color: #00FFFF; ; font-family: 'Courier New', Courier""",
'4':"""background-color: #FF00FF; ; font-family: 'Courier New', Courier""",
}
self.color_map_rgb = {
'color_1':(0.0,0.0,1.0),
'color_2':(1.0,1.0,0.0),
'color_3':(0.0,1.0,1.0),
'color_4':(1.0,0.0,1.0),
}
def test_getColorMapS0(self):
"""tests for getColorMapS0"""
mf = MotifFormatter()
module_ids = ['1','2','3','4']
self.assertEqual(mf.getColorMapS0(module_ids),self.color_map)
def test_getColorMap(self):
"""tests for getColorMap"""
mf = MotifFormatter()
self.assertEqual(mf.getColorMap(self.motif_results),self.color_map)
def test_getColorMapRgb(self):
"""tests for getColorMapRgb"""
mf = MotifFormatter()
self.assertEqual(mf.getColorMapRgb(self.motif_results),\
self.color_map_rgb)
#run if called from command-line
if __name__ == "__main__":
main()
