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#!/usr/bin/env python
# Author: Greg Caporaso (gregcaporaso@gmail.com)
# test_recode_alignment.py
""" Description
File created on 19 Jun 2007.
"""
from __future__ import division
from numpy import array
from cogent import LoadSeqs
from cogent.util.unit_test import TestCase, main
from cogent.core.alignment import DenseAlignment
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel
from cogent.core.alphabet import Alphabet
from cogent.app.gctmpca import gctmpca_aa_order,\
default_gctmpca_aa_sub_matrix
from cogent.util.recode_alignment import alphabets, recode_dense_alignment,\
build_alphabet_map, recode_freq_vector, recode_alignment,\
recode_counts_and_freqs, recode_count_matrix
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Beta"
class RecodeAlignmentTests(TestCase):
""" Tests of functions in recode_alphabet.py
These functions will probably move at some point, and the unit tests
will move with them.
"""
def setUp(self):
""" Initialize some variables for the tests """
self.canonical_abbrevs = 'ACDEFGHIKLMNPQRSTVWY'
self.ambiguous_abbrevs = 'BXZ'
self.all_to_a = [('A',self.canonical_abbrevs+\
self.ambiguous_abbrevs)]
self.charge_2 = alphabets['charge_2']
self.hydropathy_3 = alphabets['hydropathy_3']
self.orig = alphabets['orig']
self.aln = DenseAlignment(\
data={'1':'CDDFBXZ', '2':'CDD-BXZ', '3':'AAAASS-'})
self.aln2 = LoadSeqs(\
data={'1':'CDDFBXZ', '2':'CDD-BXZ', '3':'AAAASS-'})
def test_build_alphabet_map_handles_bad_data(self):
"""build_alphabet_map: bad data raises error """
self.assertRaises(ValueError,build_alphabet_map)
self.assertRaises(ValueError,build_alphabet_map,'not_a_valid_id')
self.assertRaises(ValueError,build_alphabet_map,\
alphabet_def=['A','BCD','B','EFG'])
def test_build_alphabet_map_w_alphabet_id(self):
"""build_alphabet_map: returns correct dict when given alphabet_id
"""
expected = dict([\
('G','G'), ('A','G'), ('V','G'), ('L','G'), ('I','G'),\
('S','G'), ('P','G'), ('T','G'), ('C','G'), ('N','G'), ('D','G'),\
('X','G'), ('B','G'), ('M','M'), ('F','M'), ('Y','M'), ('W','M'),\
('Q','M'), ('K','M'), ('H','M'), ('R','M'), ('E','M'), ('Z','M')])
self.assertEqual(build_alphabet_map('size_2'),expected)
self.assertEqual(build_alphabet_map('charge_3')['E'],'D')
self.assertEqual(build_alphabet_map('charge_3')['B'],'A')
self.assertEqual(build_alphabet_map('charge_3')['K'],'K')
def test_build_alphabet_map_w_alphabet_def(self):
"""build_alphabet_map: returns correct dict when given alphabet_def
"""
expected = dict([\
('G','S'), ('A','S'), ('V','S'), ('L','S'), ('I','S'),\
('S','S'), ('P','S'), ('T','S'), ('C','S'), ('N','S'), ('D','S'),\
('X','S'), ('B','S'), ('M','L'), ('F','L'), ('Y','L'), ('W','L'),\
('Q','L'), ('K','L'), ('H','L'), ('R','L'), ('E','L'), ('Z','L')])
self.assertEqual(build_alphabet_map(alphabet_def=\
[('S','GAVLISPTCNDXB'),('L','MFYWQKHREZ')]),expected)
def test_build_alphabet_map_handles_all_ids_and_defs_wo_error(self):
"""build_alphabet_map: handles all pre-defined alphabets w/o error"""
for alphabet_id, alphabet_def in alphabets.items():
try:
build_alphabet_map(alphabet_id=alphabet_id)
except ValueError:
raise AssertionError, "Failed on id: %s" % alphabet_id
try:
build_alphabet_map(alphabet_def=alphabet_def)
except ValueError:
raise AssertionError, "Failed on def: %s" % str(alphabet_def)
def test_recode_dense_alignment_handles_all_ids_and_defs_wo_error(self):
"""recode_dense_alignment: handles pre-defined alphabets w/o error"""
for alphabet_id, alphabet_def in alphabets.items():
try:
recode_dense_alignment(self.aln,alphabet_id=alphabet_id)
except ValueError:
raise AssertionError, "Failed on id: %s" % alphabet_id
try:
recode_dense_alignment(self.aln,alphabet_def=alphabet_def)
except ValueError:
raise AssertionError, "Failed on def: %s" % str(alphabet_def)
def test_recode_dense_alignment_leaves_original_alignment_intact(self):
"""recode_dense_alignment: leaves input alignment intact
"""
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertNotEqual(actual,self.aln)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertNotEqual(actual,self.aln)
def test_recode_dense_alignment(self):
"""recode_dense_alignment: recode alignment to charge_2 alpha works
"""
expected_c2 = DenseAlignment(data=\
{'1':'AKKAKAK','2':'AKK-KAK','3':'AAAAAA-'})
expected_h3 = DenseAlignment(data=\
{'1':'PRRPRPR','2':'PRR-RPR','3':'PPPPYY-'})
expected_aa = DenseAlignment(data=\
{'1':'AAAAAAA','2':'AAA-AAA','3':'AAAAAA-'})
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertEqual(actual,expected_c2)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertEqual(actual,expected_c2)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_id='hydropathy_3')
self.assertEqual(actual,expected_h3)
actual = recode_dense_alignment(self.aln,\
alphabet_def=self.hydropathy_3)
self.assertEqual(actual,expected_h3)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_def=self.all_to_a)
self.assertEqual(actual,expected_aa)
# original charactars which aren't remapped are let in original state
actual = recode_dense_alignment(self.aln, alphabet_def=[('a','b')])
self.assertEqual(actual,self.aln)
# non-alphabetic character mapped same as alphabetic characters
actual = recode_dense_alignment(self.aln, alphabet_def=[('.','-')])
expected = DenseAlignment(\
data={'1':'CDDFBXZ', '2':'CDD.BXZ', '3':'AAAASS.'})
self.assertEqual(actual,expected)
def test_recode_dense_alignment_to_orig(self):
"""recode_dense_alignment: recode aln to orig returns original aln
"""
# provided with alphabet_id
self.assertEqual(recode_dense_alignment(\
self.aln, alphabet_id='orig'), self.aln)
# provided with alphabet_def
self.assertEqual(recode_dense_alignment(\
self.aln, alphabet_def=self.orig), self.aln)
# THE FUNCTION THAT THESE TESTS APPLY TO ONLY EXISTS AS A STUB RIGHT
# NOW -- WILL UNCOMMENT THE TESTS WHEN THE FUNCTIONS IS READY.
# --GREG C. (11/19/08)
# def test_recode_alignment(self):
# """recode_alignment: recode alignment works as expected
# """
# expected_c2 = LoadSeqs(data=\
# {'1':'AKKAKAK','2':'AKK-KAK','3':'AAAAAA-'})
# expected_h3 = LoadSeqs(data=\
# {'1':'PRRPRPR','2':'PRR-RPR','3':'PPPPYY-'})
# expected_aa = LoadSeqs(data=\
# {'1':'AAAAAAA','2':'AAA-AAA','3':'AAAAAA-'})
#
# # provided with alphabet_id
# actual = recode_alignment(self.aln2, alphabet_id='charge_2')
# self.assertEqual(actual,expected_c2)
# # provided with alphabet_def
# actual = recode_alignment(self.aln2, alphabet_def=self.charge_2)
# self.assertEqual(actual,expected_c2)
#
# # different alphabet
# actual = recode_alignment(self.aln2, alphabet_id='hydropathy_3')
# self.assertEqual(actual,expected_h3)
# actual = recode_alignment(self.aln2,\
# alphabet_def=self.hydropathy_3)
# self.assertEqual(actual,expected_h3)
#
# # different alphabet
# actual = recode_alignment(self.aln2, alphabet_def=self.all_to_a)
# self.assertEqual(actual,expected_aa)
#
# # original charactars which aren't remapped are let in original state
# actual = recode_alignment(self.aln2, alphabet_def=[('a','b')])
# self.assertEqual(actual,self.aln2)
#
# # non-alphabetic character mapped same as alphabetic characters
# actual = recode_alignment(self.aln2, alphabet_def=[('.','-')])
# expected = LoadSeqs(\
# data={'1':'CDDFBXZ', '2':'CDD.BXZ', '3':'AAAASS.'})
# self.assertEqual(actual,expected)
#
# def test_recode_alignment_to_orig(self):
# """recode_alignment: recode aln to orig returns original aln
# """
# # provided with alphabet_id
# self.assertEqual(recode_alignment(\
# self.aln2, alphabet_id='orig'), self.aln2)
# # provided with alphabet_def
# self.assertEqual(recode_alignment(\
# self.aln2, alphabet_def=self.orig), self.aln2)
#
# def test_recode_alignment_leaves_original_alignment_intact(self):
# """recode_alignment: leaves input alignment intact
# """
# # provided with alphabet_id
# actual = recode_alignment(self.aln2, alphabet_id='charge_2')
# self.assertNotEqual(actual,self.aln2)
# # provided with alphabet_def
# actual = recode_alignment(self.aln2, alphabet_def=self.charge_2)
# self.assertNotEqual(actual,self.aln2)
def test_recode_freq_vector(self):
"""recode_freq_vector: bg freqs updated to reflect recoded alphabet
"""
freqs = {'A':0.21, 'E':0.29, 'C':0.05, 'D':0.45}
a_def = [('A','AEC'),('E','D')]
expected = {'A':0.55, 'E':0.45}
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
expected)
# reversal of alphabet
freqs = {'A':0.21, 'E':0.29, 'C':0.05, 'D':0.45}
a_def = [('A','D'),('E','C'),('C','E'),('D','A')]
expected = {'A':0.45,'E':0.05,'C':0.29,'D':0.21}
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
expected)
# no change in freqs (old alphabet = new alphabet)
freqs = {'A':0.21, 'E':0.29, 'C':0.05, 'D':0.45}
a_def = [('A','A'),('E','E'),('C','C'),('D','D')]
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
freqs)
freqs = {'A':0.21, 'E':0.29, 'C':0.05, 'D':0.45}
a_def = [('X','AEC'),('Y','D')]
expected = {'X':0.55, 'Y':0.45}
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
expected)
def test_recode_freq_vector_ignores(self):
"""recode_freq_vector: ignored chars are ignored
"""
freqs = {'A':0.21, 'B':0.29, 'C':0.05, 'D':0.45,'X':0.22,'Z':0.5}
a_def = [('A','A'),('B','B'),('C','C'),('D','D'),('X','X'),('Z','Z')]
expected = {'A':0.21,'C':0.05, 'D':0.45}
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
expected)
freqs = {'D':0.21, 'E':0.29, 'N':0.05,\
'Q':0.45,'B':0.26,'Z':0.74,'X':1.0}
a_def = [('D','DEN'),('Q','Q')]
expected = {'D':0.55, 'Q':0.45}
self.assertFloatEqual(recode_freq_vector(a_def,freqs),\
expected)
class RecodeMatrixTests(TestCase):
""" Tests of substitution matrix recoding. """
def setUp(self):
""" Create variables for use in the tests """
self.m1 = [[0,4,1,3,5],[4,0,2,4,6],[1,2,0,7,8],[3,4,7,0,9],[5,6,8,9,0]]
self.recoded_m1 =\
[[0,0,21,0,0],[0,0,0,0,0],[21,0,0,0,0],[0,0,0,0,0],[0,0,0,0,0]]
self.aa_order1 = 'DELIV'
self.input_freqs1 = dict(zip(self.aa_order1,[0.2]*5))
self.alphabet1 = [('D','DE'),('L','LIV')]
#create_recoded_rate_matrix(alphabets['a1_4'])
self.m2 = [[0,8,6,5,1],[8,0,7,3,0],[6,7,0,4,2],[5,3,4,0,0],[1,0,2,0,0]]
self.recoded_m2 =\
[[0,0,21,0,1],[0,0,0,0,0],[21,0,0,0,2],[0,0,0,0,0],[1,0,2,0,0]]
self.aa_order2 = 'DELIC'
self.input_freqs2 = dict(zip(self.aa_order2,[0.2]*5))
self.alphabet2 = [('D','DE'),('L','LI'),('C','C')]
self.alphabet2_w_ambig = [('D','DEX'),('L','LIB'),('C','CZ')]
def test_recode_counts_and_freqs(self):
"""recode_counts_and_freqs: functions as expected
"""
alphabet = alphabets['charge_his_3']
aa_order = 'ACDEFGHIKLMNPQRSTVWY'
actual = recode_counts_and_freqs(alphabet)
expected_matrix = recode_count_matrix(alphabet,\
count_matrix=DSO78_matrix,aa_order=aa_order)
expected_freqs = {}.fromkeys(aa_order,0.0)
expected_freqs.update(recode_freq_vector(alphabet,DSO78_freqs))
expected = (expected_matrix,expected_freqs)
self.assertEqual(actual,expected)
def test_recode_count_matrix_2_states(self):
"""recode_count_matrix: returns correct result with 2-state alphabet
"""
actual = recode_count_matrix(self.alphabet1,self.m1,self.aa_order1)
expected = self.recoded_m1
self.assertEqual(actual,expected)
def test_recode_count_matrix_3_states(self):
"""recode_count_matrix: returns correct result with 3-state alphabet
"""
actual = recode_count_matrix(self.alphabet2,self.m2,self.aa_order2)
expected = self.recoded_m2
self.assertEqual(actual,expected)
def test_recode_count_matrix_3_states_ambig_ignored(self):
"""recode_count_matrix: correct result w 3-state alphabet w ambig chars
"""
actual =\
recode_count_matrix(self.alphabet2_w_ambig,self.m2,self.aa_order2)
expected = self.recoded_m2
self.assertEqual(actual,expected)
def test_recode_count_matrix_no_change(self):
"""recode_count_matrix: no changes applied when they shouldn't be
"""
# recoding recoded matrices
actual =\
recode_count_matrix(self.alphabet1,self.recoded_m1,self.aa_order1)
expected = self.recoded_m1
self.assertEqual(actual,expected)
actual =\
recode_count_matrix(self.alphabet2,self.recoded_m2,self.aa_order2)
expected = self.recoded_m2
self.assertEqual(actual,expected)
if __name__ == "__main__":
main()
|
