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#!/usr/bin/env python
from __future__ import division
from numpy import array, transpose, alltrue
from cogent.util.unit_test import TestCase, main
from cogent.core.moltype import RNA
from cogent.core.sequence import RnaSequence, Sequence, ModelSequence
from cogent.core.alignment import Alignment, DenseAlignment
__author__ = "Sandra Smit"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Sandra Smit", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Sandra Smit"
__email__ = "sandra.smit@colorado.edu"
__status__ = "Production"
class AllTests(TestCase):
def setUp(self):
"""setUp method for all tests"""
# named sequences
self.rna1 = RnaSequence('UCAGGG', Name='rna1')
self.rna2 = RnaSequence('YCU-RG', Name='rna2')
self.rna3 = RnaSequence('CAA-NR', Name='rna3')
self.model1 = ModelSequence('UCAGGG', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
self.model2 = ModelSequence('YCU-RG', Name='rna2',\
Alphabet=RNA.Alphabets.DegenGapped)
self.model3 = ModelSequence('CAA-NR', Name='rna3',\
Alphabet=RNA.Alphabets.DegenGapped)
self.aln = Alignment([self.rna1, self.rna2, self.rna3], MolType=RNA)
self.da = DenseAlignment([self.model1, self.model2, self.model3],\
MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
# seqs no name
self.nn_rna1 = RnaSequence('UCAGGG')
self.nn_rna2 = RnaSequence('YCU-RG')
self.nn_rna3 = RnaSequence('CAA-NR')
self.nn_model1 = ModelSequence('UCAGGG',\
Alphabet=RNA.Alphabets.DegenGapped)
self.nn_model2 = ModelSequence('YCU-RG',\
Alphabet=RNA.Alphabets.DegenGapped)
self.nn_model3 = ModelSequence('CAA-NR',\
Alphabet=RNA.Alphabets.DegenGapped)
self.nn_aln = Alignment([self.nn_rna1, self.nn_rna2, self.nn_rna3],\
MolType=RNA)
self.nn_da = DenseAlignment([self.nn_model1, self.nn_model2,\
self.nn_model3], MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
def test_printing_named_seqs(self):
"""Printing named seqs should work the same on Aln and DenseAln"""
#Note: the newline trailing each sequence is intentional, because
#we want each FASTA-format record to be separated.
exp_lines_general = ['>rna1','UCAGGG','>rna2','YCU-RG','>rna3','CAA-NR']
self.assertEqual(str(self.aln), '\n'.join(exp_lines_general) + '\n')
self.assertEqual(str(self.da), '\n'.join(exp_lines_general) + '\n')
def test_printing_unnamed_seqs(self):
"""Printing unnamed sequences should work the same on Aln and DenseAln
"""
exp_lines_gen = ['>seq_0','UCAGGG','>seq_1','YCU-RG','>seq_2','CAA-NR\n']
self.assertEqual(str(self.nn_aln),'\n'.join(exp_lines_gen))
self.assertEqual(str(self.nn_da),'\n'.join(exp_lines_gen))
def test_DenseAlignment_without_moltype(self):
"""Expect MolType to be picked up from the sequences."""
m1 = ModelSequence('UCAG',Alphabet=RNA.Alphabets.DegenGapped,\
Name='rna1')
m2 = ModelSequence('CCCR',Alphabet=RNA.Alphabets.DegenGapped,\
Name='rna2')
da = DenseAlignment([m1, m2])
exp_lines = ['>rna1','UCAG','>rna2','CCCR']
self.assertEqual(str(da), '\n'.join(exp_lines) + '\n')
def test_names(self):
# Should both alignments handle names the same way?
self.assertEqual(self.aln.Names, ['rna1','rna2','rna3'])
self.assertEqual(self.da.Names, ['rna1','rna2','rna3'])
# On unnamed sequences the behavior is now the same.
self.assertEqual(self.nn_aln.Names, ['seq_0','seq_1','seq_2'])
self.assertEqual(self.nn_da.Names, ['seq_0','seq_1','seq_2'])
def test_seqFreqs(self):
"""seqFreqs should work the same on Alignment and DenseAlignment"""
# Used alphabet: ('U', 'C', 'A', 'G', '-', 'B', 'D', 'H',\
# 'K', 'M', 'N', 'S', 'R', 'W', 'V', 'Y')
exp = [[1,1,1,3,0,0,0,0,0,0,0,0,0,0,0,0,0],\
[1,1,0,1,1,0,0,0,0,0,0,0,1,0,0,1,0],\
[0,1,2,0,1,0,0,0,0,0,1,0,1,0,0,0,0]]
# This works
self.assertEqual(self.da.getSeqFreqs().Data, exp)
# This used to raise an error, but now works
self.assertEqual(self.aln.getSeqFreqs().Data, exp)
def test_subset_positions_DenseAlignment(self):
model1 = ModelSequence('UCG', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
model2 = ModelSequence('YCG', Name='rna2',\
Alphabet=RNA.Alphabets.DegenGapped)
model3 = ModelSequence('CAR', Name='rna3',\
Alphabet=RNA.Alphabets.DegenGapped)
sub_da = DenseAlignment([model1, model2, model3],\
MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
full_data = array([[0,1,2,3,3,3],[15,1,0,4,12,3],[1,2,2,4,10,12]])
sub_data = array([[0,1,3],[15,1,3],[1,2,12]])
# First check some data
self.assertEqual(self.da.ArraySeqs, full_data)
self.assertEqual(self.da.ArrayPositions, transpose(full_data))
self.assertEqual(sub_da.ArraySeqs, sub_data)
self.assertEqual(sub_da.ArrayPositions, transpose(sub_data))
obs_sub_da_TP = self.da.takePositions([0,1,5])
obs_sub_da_SA = self.da.getSubAlignment(pos=[0,1,5])
# When using the getSubAlignment method the data is right
self.assertEqual(obs_sub_da_SA, sub_da)
self.failIfEqual(obs_sub_da_SA, self.da)
self.assertEqual(obs_sub_da_SA.ArraySeqs, sub_data)
self.assertEqual(obs_sub_da_SA.ArrayPositions, transpose(sub_data))
# For the takePositions method: Why does this work
self.assertEqual(obs_sub_da_TP, sub_da)
self.failIfEqual(obs_sub_da_TP, self.da)
# If the data doesn't match?
self.assertEqual(obs_sub_da_TP.ArraySeqs, sub_data)
self.assertEqual(obs_sub_da_TP.ArrayPositions, transpose(sub_data))
# Shouldn't the __eq__ method check the data at least?
def test_subset_positions_Alignment(self):
rna1 = RnaSequence('UCG', Name='rna1')
rna2 = RnaSequence('YCG', Name='rna2')
rna3 = RnaSequence('CAR', Name='rna3')
sub_aln = Alignment([rna1, rna2, rna3], MolType=RNA)
obs_sub_aln = self.aln.takePositions([0,1,5])
self.assertEqual(obs_sub_aln, sub_aln)
self.failIfEqual(obs_sub_aln, self.aln)
# string representations should be the same. This fails right
# now, because sequence order is not maintained. See separate test.
self.assertEqual(str(obs_sub_aln), str(sub_aln))
def test_takePositions_sequence_order(self):
"""Alignment takePositions should maintain seq order"""
#This works
self.assertEqual(self.da.Names,['rna1','rna2','rna3'])
sub_da = self.da.getSubAlignment(pos=[0,1,5])
self.assertEqual(sub_da.Names,['rna1','rna2','rna3'])
# seq order not maintained in Alignment
self.assertEqual(self.aln.Names,['rna1','rna2','rna3'])
sub_aln = self.aln.takePositions([0,1,5])
self.assertEqual(sub_aln.Names,['rna1','rna2','rna3'])
def test_subset_seqs_Alignment(self):
rna1 = RnaSequence('UCG', Name='rna1')
rna2 = RnaSequence('YCG', Name='rna2')
rna3 = RnaSequence('CAR', Name='rna3')
sub_aln = Alignment([rna2, rna3], MolType=RNA)
aln = Alignment([rna1, rna2, rna3], MolType=RNA)
obs_sub_aln = aln.takeSeqs(['rna2','rna3'])
self.assertEqual(obs_sub_aln, sub_aln)
self.assertEqual(str(obs_sub_aln), str(sub_aln))
# Selected sequences should be in specified order?
obs_sub_aln_1 = self.aln.takeSeqs(['rna3','rna2'])
obs_sub_aln_2 = self.aln.takeSeqs(['rna2','rna3'])
self.failIfEqual(str(obs_sub_aln_1), str(obs_sub_aln_2))
def test_subset_seqs_DenseAlignment(self):
model1 = ModelSequence('UCG', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
model2 = ModelSequence('YCG', Name='rna2',\
Alphabet=RNA.Alphabets.DegenGapped)
model3 = ModelSequence('CAR', Name='rna3',\
Alphabet=RNA.Alphabets.DegenGapped)
sub_da = DenseAlignment([model1, model2, model3],\
MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
# takeSeqs by name should have the same effect as
# getSubAlignment by seq idx?
obs_sub_da_TS = self.da.takeSeqs(['rna1'])
obs_sub_da_SA = self.da.getSubAlignment(seqs=[0])
# These two are now the same. Fixed mapping of key to char array.
self.assertEqual(obs_sub_da_TS, obs_sub_da_SA)
self.assertEqual(str(obs_sub_da_TS), str(obs_sub_da_SA))
def test_aln_equality(self):
# When does something compare equal?
self.assertEqual(self.da == self.da, True)
# one sequence less
other_da1 = DenseAlignment([self.model1, self.model2],\
MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
self.assertEqual(self.da == other_da1, False)
# seqs in different order -- doesn't matter
other_da2 = DenseAlignment([self.model1, self.model3, self.model2],\
MolType=RNA, Alphabet=RNA.Alphabets.DegenGapped)
self.assertEqual(self.da == other_da2, True)
# seqs in different encoding -- doesn't matter, only looks at data
other_da3 = DenseAlignment([self.model1, self.model2, self.model3])
# Should this compare False even though the data is exactly the same?
# The MolType is different...
self.assertEqual(self.da == other_da3, True)
assert alltrue(map(alltrue,self.da.ArraySeqs == other_da3.ArraySeqs))
def test_seq_equality(self):
model1 = ModelSequence('UCG', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
model2 = ModelSequence('UCG', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
# Shouldn't the above two sequences be equal?
self.assertEqual(model1, model2)
# string comparison is True
self.assertEqual(str(model1), str(model2))
def test_seq_ungapping(self):
rna1 = RnaSequence('U-C-A-G-', Name='rna1')
model1 = ModelSequence('U-C-A-G-', Name='rna1',\
Alphabet=RNA.Alphabets.DegenGapped)
self.assertEqual(rna1, 'U-C-A-G-')
self.assertEqual(rna1.degap(), 'UCAG')
# check is produces the right string from the beginning
self.assertEqual(str(model1), 'U-C-A-G-')
self.assertEqual(model1._data, [0,4,1,4,2,4,3,4])
# ModelSequence should maybe have the same degap method as normal Seq
self.assertEqual(str(model1.degap()), 'UCAG')
def test_the_rest_of_ModelSequence(self):
"""The class ModelSequence has 14 methods, but only 2 unittests.
You might want to add some tests there..."""
#note: mostly these are tested in derived classes, for convenience.
pass
if __name__ == "__main__":
main()
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