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#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2010 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
from gt.core import *
import unittest
import tempfile
import os
import string
class AlphabetTest(unittest.TestCase):
def setUp(self):
self.dnaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False)
self.dnaseqfile.write(">seq1\nagtccagctgtcagctagcgggcccgatgatatttt")
self.aaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False)
self.aaseqfile.write(">seq1\nMVHFTAEEKAAVTSLWSKMNVEEAGGEALG")
self.dnaal1file = tempfile.NamedTemporaryFile(mode="w", suffix=".al1",
delete=False)
self.dnaal1file.write("aA\ncC\ngG\ntTuU\nnsywrkvbdhmNSYWRKVBDHM\n")
self.aaal1file = tempfile.NamedTemporaryFile(mode="w", suffix=".al1",
delete=False)
self.aaal1file.write(
"L\nV\nI\nF\nK\nR\nE\nD\nA\nG\nS\nT\nN\nQ\nY\nW\nP\nH\nM\nC\nXUBZO*- x\n")
self.dnaseqfile.close()
self.aaseqfile.close()
self.dnaal1file.close()
self.aaal1file.close()
def tearDown(self):
os.unlink(self.dnaseqfile.name)
os.unlink(self.aaseqfile.name)
os.unlink(self.dnaal1file.name)
os.unlink(self.aaal1file.name)
def dna_encodedecode(self, a_dna):
# test DNA alphabet
dnachars = {0: ('A', 'a'), 1: ('C', 'c'), 2: ('G', 'g'),
3: ('T', 't'), 254: ('N', 'n')}
# encoding should yield the correct code independent of case
for idx, c in dnachars.items():
self.assertEqual(a_dna.encode(c[0]), idx)
self.assertEqual(a_dna.decode(a_dna.encode(c[0])), c[1])
self.assertEqual(a_dna.encode(c[1]), idx)
self.assertEqual(a_dna.decode(a_dna.encode(c[1])), c[1])
# invalid input should raise an exception
self.assertRaises(GTError, a_dna.encode, 'Z')
teststr = "agtccagctgtcagctagcgggcccgatgatatttt"
# encode string 'by hand'
encodedstr = [a_dna.encode(c) for c in teststr]
# ensure that string is ok
self.assertEqual(a_dna.decode_seq(encodedstr), teststr)
def protein_encodedecode(self, a_protein):
# test AA alphabet
aas = "LVIFKREDAGSTNQYWPHMC"
aachars = {}
for idx, c in enumerate(aas):
aachars[idx] = (c.upper(), c.lower())
# print aachars
wcs = ('X', 'x', 'U', 'u', 'B', 'b', 'Z', 'z', 'O', '*', '-')
# encoding should yield the correct code independent of case
for idx, c in aachars.items():
self.assertEqual(a_protein.encode(c[0]), idx)
self.assertEqual(a_protein.decode(a_protein.encode(c[0])), c[0])
# invalid input should raise an exception
self.assertRaises(GTError, a_protein.encode, '&')
teststr = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG"
# encode string 'by hand'
encodedstr = [a_protein.encode(c) for c in teststr]
# ensure that string is ok
self.assertEqual(a_protein.decode_seq(encodedstr), teststr)
def test_dna_newcreated(self):
a_dna = Alphabet.create_dna()
self.dna_encodedecode(a_dna)
def test_dna_fromsequence(self):
a_dna = Alphabet.create_from_sequence([self.dnaseqfile.name])
self.dna_encodedecode(a_dna)
def test_dna_fromsequence_fail(self):
self.assertRaises(TypeError, Alphabet.create_from_sequence,
self.dnaseqfile.name)
def test_dna_fromal1file(self):
indexname = self.dnaal1file.name.rsplit('.', 1)[0]
a_dna = Alphabet.create_from_file(indexname)
self.dna_encodedecode(a_dna)
def test_dna_fromal1file_fail(self):
self.assertRaises(IOError, Alphabet.create_from_file, "nonexisting")
def test_aa_newcreated(self):
a_protein = Alphabet.create_protein()
self.protein_encodedecode(a_protein)
def test_aa_isdna(self):
a_protein = Alphabet.create_protein()
self.assertTrue(a_protein.is_protein())
self.assertFalse(a_protein.is_dna())
def test_isdna(self):
a_protein = Alphabet.create_dna()
self.assertFalse(a_protein.is_protein())
self.assertTrue(a_protein.is_dna())
def test_aa_fromsequence(self):
a_protein = Alphabet.create_from_sequence([self.aaseqfile.name])
self.protein_encodedecode(a_protein)
def test_aa_fromsequence_fail(self):
self.assertRaises(TypeError, Alphabet.create_from_sequence,
self.aaseqfile.name)
def test_aa_fromsequence_fail_2(self):
self.assertRaises(IOError, Alphabet.create_from_sequence,
["nonexisting"])
def test_aa_fromal1file(self):
indexname = self.aaal1file.name.rsplit('.', 1)[0]
a_protein = Alphabet.create_from_file(indexname)
self.protein_encodedecode(a_protein)
def test_aa_fromal1file_fail(self):
self.assertRaises(IOError, Alphabet.create_from_file, "nonexisting")
if __name__ == "__main__":
unittest.main()
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