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# Copyright 2015 by Peter Cock. All rights reserved.
# Copyright 2015 by Antony Lee. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Testing online code for Bio.motifs (weblogo etc)."""
import os
import unittest
# We want to test these:
from Bio import motifs
# In order to check any sequences returned
from Bio.Seq import Seq
import requires_internet
requires_internet.check()
class TestotifWeblogo(unittest.TestCase):
"""Tests Bio.motifs online code."""
def check(self, seqs_as_strs, alpha):
# Using Seq objects:
m = motifs.create([Seq(s) for s in seqs_as_strs], alpha)
m.weblogo(os.devnull)
# Using strings:
m = motifs.create(seqs_as_strs, alpha)
m.weblogo(os.devnull)
def test_dna(self):
"""Test Bio.motifs.weblogo with a DNA sequence."""
self.check(
["TACAA", "TACGC", "TACAC", "TACCC", "AACCC", "AATGC", "AATGC"], "GATCBDSW"
)
def test_rna(self):
"""Test Bio.motifs.weblogo with an RNA sequence."""
self.check(
["UACAA", "UACGC", "UACAC", "UACCC", "AACCC", "AAUGC", "AAUGC"], "GAUC"
)
def test_protein(self):
"""Test Bio.motifs.weblogo with a protein sequence."""
self.check(
["ACDEG", "AYCRN", "HYLID", "AYHEL", "ACDEH", "AYYRN", "HYIID"],
"ACDEFGHIKLMNPQRSTVWYBXZJUO",
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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