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# Copyright (C) 2013 by Zheng Ruan (zruan1991@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for the Bio.codonalign modules.
"""
import warnings
import tempfile
import unittest
from Bio import BiopythonWarning, BiopythonExperimentalWarning
from Bio import SeqIO
from Bio import AlignIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
from Bio.Align import MultipleSeqAlignment
from Bio.Data import CodonTable
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio import codonalign
TEST_ALIGN_FILE1 = [('codonalign/nucl1.fa', 'codonalign/pro1.aln'), 'parse']
TEST_ALIGN_FILE2 = [('codonalign/nucl2.fa', 'codonalign/pro2.aln'), 'parse']
TEST_ALIGN_FILE3 = [('codonalign/nucl3.fa', 'codonalign/pro3.aln'), 'index']
TEST_ALIGN_FILE4 = [('codonalign/nucl4.fa', 'codonalign/pro4.aln'), 'index']
TEST_ALIGN_FILE5 = [('codonalign/nucl5.fa', 'codonalign/pro5.aln'), 'parse']
TEST_ALIGN_FILE6 = [('codonalign/egfr_nucl.fa', 'codonalign/egfr_pro.aln', 'codonalign/egfr_id'), 'id']
TEST_ALIGN_FILE7 = [('codonalign/drosophilla.fasta', 'codonalign/adh.aln'), 'index']
temp_dir = tempfile.mkdtemp()
class TestCodonSeq(unittest.TestCase):
def test_seq(self):
codonseq1 = codonalign.CodonSeq('AAATTT---TTTGGACCC', rf_table=[0, 3, 6, 9, 12])
self.assertEqual(len(codonseq1), 18)
self.assertEqual(codonseq1.get_codon_num(), 5)
self.assertEqual(str(codonseq1.get_codon(0)), 'AAA')
self.assertEqual(str(codonseq1.get_codon(-1)), 'CCC')
self.assertEqual(str(codonseq1.get_codon(slice(1, 3))), 'TTT---')
self.assertEqual(str(codonseq1.get_codon(slice(None, None, -1))), 'CCCGGATTT---TTTAAA')
self.assertRaises(ValueError, codonalign.CodonSeq, 'AAA-TT')
self.assertRaises(AssertionError, codonalign.CodonSeq, 'AAA-T')
self.assertRaises(ValueError, codonalign.CodonSeq, 'YVVRRDQQQ')
self.assertTrue(isinstance(codonseq1.toSeq(), Seq))
class TestCodonAlignment(unittest.TestCase):
def setUp(self):
codonseq1 = codonalign.CodonSeq('AAATTT---TTTGGACCC', codonalign.default_codon_alphabet)
codonseq2 = codonalign.CodonSeq('AAGTTT---TTTGGGCCC', codonalign.default_codon_alphabet)
codonseq3 = codonalign.CodonSeq('AAGTAT---TTTGGACCC', codonalign.default_codon_alphabet)
codonseq4 = codonalign.CodonSeq('AACTTT---TTTGGACGC', codonalign.default_codon_alphabet)
self.seqrec = [SeqRecord(codonseq1, id="alpha"),
SeqRecord(codonseq2, id="beta"),
SeqRecord(codonseq3, id="gamma"),
SeqRecord(codonseq4, id="delta")]
def test_align(self):
codonAlign = codonalign.CodonAlignment(self.seqrec)
self.assertEqual(codonAlign.get_aln_length(), 6)
self.assertTrue(isinstance(codonAlign.toMultipleSeqAlignment(), MultipleSeqAlignment))
class TestBuildAndIO(unittest.TestCase):
def setUp(self):
self.aln_file = [TEST_ALIGN_FILE1,
TEST_ALIGN_FILE2,
TEST_ALIGN_FILE3,
TEST_ALIGN_FILE4,
TEST_ALIGN_FILE5,
TEST_ALIGN_FILE6]
alns = []
for i in self.aln_file:
if i[1] == 'parse':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet)
elif i[1] == 'index':
nucl = SeqIO.index(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet, max_score=20)
elif i[1] == 'id':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with open(i[0][2]) as handle:
id = dict((i.split()[0], i.split()[1]) for i in handle)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, corr_dict=id, alphabet=codonalign.default_codon_alphabet)
alns.append(caln)
nucl.close() # Close the indexed FASTA file
self.alns = alns
def test_IO(self):
self.assertEqual(len(self.alns), 6)
# print temp_dir
for n, i in enumerate(self.alns):
aln = i.toMultipleSeqAlignment()
AlignIO.write(aln, temp_dir + '/aln' + str(n) + '.clw', 'clustal')
class Test_build(unittest.TestCase):
def setUp(self):
# Test set 1
seq1 = SeqRecord(Seq('TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG',
alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro1')
seq2 = SeqRecord(Seq('TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG',
alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro2')
pro1 = SeqRecord(Seq('SGTARTKLLLLLAALCAAGGALE', alphabet=IUPAC.protein), id='pro1')
pro2 = SeqRecord(Seq('SGTSRTKRLLLLAALGAAGGALE', alphabet=IUPAC.protein), id='pro2')
aln1 = MultipleSeqAlignment([pro1, pro2])
self.aln1 = aln1
self.seqlist1 = [seq1, seq2]
# Test set 2
# M K K H E L(F)L C Q G T S N K L T Q(L)L G T F E D H F L S L Q R M F N N C E V V
seq3 = SeqRecord(Seq('ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro1')
# seq4 =SeqRecord(Seq('ATGAAAAAGCACGAGTT CTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAA TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro2')
seq4 = SeqRecord(Seq('ATGAAAAAGCACGAGTTCTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAATGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro2')
# seq5 =SeqRecord(Seq('ATGAAAAAGCACGAGTT CTTTGCCAAGGGACAAGTAACAAGCTCACCC TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro3')
seq5 = SeqRecord(Seq('ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro3')
pro3 = SeqRecord(Seq('MKKHELLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL', alphabet=IUPAC.protein), id='pro1')
pro4 = SeqRecord(Seq('MKKHEFLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL', alphabet=IUPAC.protein), id='pro2')
pro5 = SeqRecord(Seq('MKKHELLCQGTSNKLTLLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL', alphabet=IUPAC.protein), id='pro3')
aln2 = MultipleSeqAlignment([pro3, pro4, pro5])
self.aln2 = aln2
self.seqlist2 = [seq3, seq4, seq5]
# Test set 3
# use Yeast mitochondrial codon table
seq6 = SeqRecord(Seq('ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACCTTTCTTTTCTCAAGACCATCCAG', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro6')
seq7 = SeqRecord(Seq('ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACGTGTCTCTGCTCAAGACCATCCAG', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro7')
seq8 = SeqRecord(Seq('ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAACCACTCTTTTCTCATGACCATCCAG', alphabet=IUPAC.IUPACUnambiguousDNA()), id='pro8')
pro6 = SeqRecord(Seq('MARDHPVGHWYDRVYLQSSNTSFTKTIQ', alphabet=IUPAC.protein), id='pro6')
pro7 = SeqRecord(Seq('MARHHPVEHWYDRVYLQSSNVSTTKTIQ', alphabet=IUPAC.protein), id='pro7')
pro8 = SeqRecord(Seq('MAGDHPVGHWYDRVYTQSSNHSFTMTIQ', alphabet=IUPAC.protein), id='pro8')
aln3 = MultipleSeqAlignment([pro6, pro7, pro8])
self.aln3 = aln3
self.seqlist3 = [seq6, seq7, seq8]
self.codontable3 = CodonTable.unambiguous_dna_by_id[3]
def test_build(self):
codon_aln1 = codonalign.build(self.aln1, self.seqlist1)
codon_aln2 = codonalign.build(self.aln2, self.seqlist2)
codon_aln3 = codonalign.build(self.aln3, self.seqlist3, codon_table=self.codontable3)
class Test_dn_ds(unittest.TestCase):
def setUp(self):
nucl = SeqIO.parse(TEST_ALIGN_FILE6[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(TEST_ALIGN_FILE6[0][1], 'clustal', alphabet=IUPAC.protein)
with open(TEST_ALIGN_FILE6[0][2]) as handle:
id_corr = dict((i.split()[0], i.split()[1]) for i in handle)
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonWarning)
aln = codonalign.build(prot, nucl, corr_dict=id_corr, alphabet=codonalign.default_codon_alphabet)
self.aln = aln
def test_dn_ds(self):
from Bio.codonalign.codonseq import cal_dn_ds
codon_seq1 = self.aln[0]
codon_seq2 = self.aln[1]
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='NG86')
self.assertAlmostEqual(round(dN, 4), 0.0209, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0178, places=4)
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='LWL85')
self.assertAlmostEqual(round(dN, 4), 0.0203, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0164, places=4)
try:
import scipy
except ImportError:
# Silently skip the rest of the test
return
# This should be present:
from scipy.linalg import expm
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='YN00')
self.assertAlmostEqual(round(dN, 4), 0.0198, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0222, places=4)
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')
self.assertAlmostEqual(round(dN, 4), 0.0194, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0217, places=4)
except ImportError:
# TODO - Show a warning?
pass
from run_tests import is_numpy
try:
from math import lgamma # New in Python 2.7
except ImportError:
lgamma = None
if is_numpy() and lgamma:
class Test_MK(unittest.TestCase):
def test_mk(self):
p = SeqIO.index(TEST_ALIGN_FILE7[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
pro_aln = AlignIO.read(TEST_ALIGN_FILE7[0][1], 'clustal', alphabet=IUPAC.protein)
codon_aln = codonalign.build(pro_aln, p)
p.close() # Close indexed FASTA file
self.assertAlmostEqual(round(codonalign.mktest([codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]), 4), 0.0021, places=4)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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