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#!/usr/bin/env python
# Copyright (c) 2006 John Gilman
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
import unittest
from weblogo.seq import (
Seq,
dna_alphabet,
nucleic_alphabet,
protein_alphabet,
reduced_protein_alphabet,
)
from weblogo.transform import (
GeneticCode,
Transform,
mask_low_complexity,
reduced_protein_alphabets,
)
class test_mask_low_complexity(unittest.TestCase):
def test_segging(self) -> None:
before = (
"mgnrafkshhghflsaegeavkthhghhdhhthfhvenhggkvalkthcgkylsigdhkqvylshhlhgdhslfhlehhg"
"gkvsikghhhhyisadhhghvstkehhdhdttfeeiii".upper()
)
after = (
"MGNRAFKSHHGHFLSAEGEAVxxxxxxxxxxxxxxxENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGG"
"KVSIKGHHHHYISADHHGHVSTKEHHDHDTTFEEIII".upper()
)
bseq = Seq(before, protein_alphabet)
aseq = Seq(after, protein_alphabet)
xseq = Seq("X" * len(bseq), protein_alphabet)
sseq = mask_low_complexity(bseq)
self.assertEqual(aseq, sseq)
# Nothing should be segged
sseq = mask_low_complexity(bseq, 12, 0, 0)
self.assertEqual(bseq, sseq)
# Everthing should be segged
sseq = mask_low_complexity(bseq, 12, 4.3, 4.3)
self.assertEqual(sseq, xseq)
mask_low_complexity(bseq, 100000, 4.3, 4.3)
def test_seg_invalid(self) -> None:
seq = Seq("KTHCGKYLSIGDHKQVYLSHH", protein_alphabet)
self.assertRaises(ValueError, mask_low_complexity, seq, 12, -1, 0)
self.assertRaises(ValueError, mask_low_complexity, seq, -1, 0, 0)
self.assertRaises(ValueError, mask_low_complexity, seq, 12, 1, 10)
self.assertRaises(ValueError, mask_low_complexity, seq, 6, 12, 13)
self.assertRaises(ValueError, mask_low_complexity, seq, 6, 2.0, 1.9)
class test_transform(unittest.TestCase):
def test_transform(self) -> None:
trans = Transform(
Seq("ACGTURYSWKMBDHVN", nucleic_alphabet),
Seq("ACGTTNNNNNNNNNNN", dna_alphabet),
)
s0 = Seq("AAAAAR", nucleic_alphabet)
s1 = trans(s0) # Callable ob
self.assertEqual(s1.alphabet, dna_alphabet)
self.assertEqual(s1, Seq("AAAAAN", dna_alphabet))
s2 = Seq(str(protein_alphabet), protein_alphabet)
self.assertRaises(ValueError, trans, s2)
# def test_translations(self) -> None:
# s = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet)
# s2 = dna_ext_to_std(s)
# s3 = Seq("ACGTTNNNNNNNNNNNACGTTNNNNNNNNNNN", dna_alphabet)
# self.assertEqual(s2, s3)
def test_reduced_protein_alphabets(self) -> None:
seq = Seq(
"ENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGGKVSIKGHHHHYISADHHGHVSTKEHHDHDT"
"TFEEIII",
reduced_protein_alphabet,
)
for t in reduced_protein_alphabets.values():
t(seq)
class test_geneticcode(unittest.TestCase):
def test_repr(self) -> None:
for t in GeneticCode.std_list():
r = repr(t)
gc = eval(r)
self.assertEqual(r, repr(gc))
self.assertEqual(str(gc), str(t))
# print r
# print t
# print gc
def test_translate_std(self) -> None:
dna = Seq("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA")
t = GeneticCode.std()
s = t.translate(dna)
self.assertEqual(str(s), "AIVMGR*KGAR")
for t in GeneticCode.std_list():
t.translate(dna)
def test_translate(self) -> None:
# Ref: http://lists.open-bio.org/pipermail/biopython/2006-March/002960.html
cft = (
(
"Vertebrate Mitochondrial",
"GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA",
"AIVMGRWKGAR",
),
(11, "CAAGGCGTCGAAYAGCTTCAGGAACAGGAC", "QGVE?LQEQD"),
(1, "GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", "AIVMGR*KGAR"),
)
for code, dna, protein in cft:
c = GeneticCode.by_name(code) # type: ignore
trans = c.translate(Seq(dna))
self.assertEqual(str(trans), protein)
self.assertRaises(ValueError, GeneticCode.by_name, "not_a_name")
def test_back_translate(self) -> None:
prot = Seq("ACDEFGHIKLMNPQRSTVWY*")
t = GeneticCode.std()
t.table["CGA"] # type: ignore
s = t.back_translate(prot)
self.assertEqual(str(prot), str(t.translate(s)))
GeneticCode.std().back_table
if __name__ == "__main__":
unittest.main()
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