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# Copyright 2015 by Peter Cock. All rights reserved.
# Copyright 2015 by Antony Lee. All rights reserved.
# 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.
"""Testing online code for Bio.motifs (weblogo etc)."""
import os
import unittest
# We want to test these:
from Bio import motifs
from Bio.Alphabet.IUPAC import extended_dna, unambiguous_rna
from Bio.Alphabet.IUPAC import extended_protein
# 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 and passing exactly the same alphabet:
m = motifs.create([Seq(s, alpha) for s in seqs_as_strs], alpha)
m.weblogo(os.devnull)
# Using Seq objects but not passing alphabet:
m = motifs.create([Seq(s, alpha) for s in seqs_as_strs])
m.weblogo(os.devnull)
# Using strings and passing alphabet:
m = motifs.create(seqs_as_strs, alpha)
m.weblogo(os.devnull)
def test_dna(self):
"""Test Bio.Motif.weblogo with a DNA sequence."""
self.check(["TACAA", "TACGC", "TACAC", "TACCC",
"AACCC", "AATGC", "AATGC"], extended_dna)
def test_rna(self):
"""Test Bio.Motif.weblogo with an RNA sequence."""
self.check(["UACAA", "UACGC", "UACAC", "UACCC",
"AACCC", "AAUGC", "AAUGC"], unambiguous_rna)
def test_protein(self):
"""Test Bio.Motif.weblogo with a protein sequence."""
self.check(["ACDEG", "AYCRN", "HYLID", "AYHEL",
"ACDEH", "AYYRN", "HYIID"], extended_protein)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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