#!/usr/bin/env python3
import unittest
import urllib.request
import os
import sys
import re
import zipfile
import warnings
import timeit
import multiprocessing
import pandas as pd
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot
import Bio.SeqIO
import Bio.pairwise2
import Bio.Entrez
import Bio.PDB
from Bio.SeqRecord import SeqRecord
from Bio.SubsMat.MatrixInfo import blosum62
class BalibaseTestCase(unittest.TestCase):
"""Base class to inherit by all test cases that need access to the balibase.
"""
def setUp(self):
balibase_zippath = "balibase.zip"
self.balibase_path = "balibase"
self.exclude_fastas = ["BBS11037.fasta"] # This one does not contain correct
# pdb codes as ids
testfile_path = os.path.join(
self.balibase_path,
"RV11.unaligned", "BBS11001.fasta")
if not os.path.isdir(self.balibase_path):
os.mkdir(self.balibase_path)
if not os.path.isfile(testfile_path):
if not os.path.isfile(balibase_zippath):
print("Fetching balibase archive from moodle...")
urllib.request.urlretrieve(
"https://moodle.polytechnique.fr/mod/resource/view.php?id=38570",
balibase_zippath)
with zipfile.ZipFile(balibase_zippath) as balibase_zip:
balibase_zip.extractall()
def get_dataset_heads(self, full=False):
"""Generator function to iterate over the first two sequences of each
unaligned fasta file.
Arguments:
full (bool): also yield the original sequences ("BB" files) and not
only the blocks of interest ("BBS")
"""
dataset_dir = os.path.join(self.balibase_path, "RV11.unaligned")
for filename in os.listdir(dataset_dir):
if filename.startswith("BBS"):
records = Bio.SeqIO.parse(
os.path.join(dataset_dir, filename),
"fasta")
seq1 = next(records)
seq2 = next(records)
if not full:
yield seq1, seq2, filename
else:
orecords = Bio.SeqIO.parse(
os.path.join(dataset_dir, "BB" + filename[3:]),
"fasta")
oseq1 = next(orecords)
oseq2 = next(orecords)
yield seq1, seq2, oseq1, oseq2, filename
def get_datasets_heads_with_struct(self):
"""Generator function to iterate over the first sequences of each
unaligned fasta file, and join the PDB to it
Returns:
Generator of (seq1, seq2, orig_seq1, orig_seq2, struct1, struct2,
name) lists, seq_ are the sequences of interest, orig_seq_ the full
sequences from which they were extracted, struct_ the PDB objects,
name the filename of the original fasta on disk (for debugging
mostly)
"""
parser = Bio.PDB.MMCIFParser()
for s1, s2, os1, os2, name in self.get_dataset_heads(full=True):
if name in self.exclude_fastas:
warnings.warn("Exluding file "+name+" according to exclusion list")
continue
item = [s1, s2, os1, os2]
for s in s1, s2:
fname = Bio.PDB.PDBList().retrieve_pdb_file(
s.id[0:4],
file_format="mmCif",
pdir="data"
)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
struct = parser.get_structure(s.id[0:4], fname)
print(fname, s.id[0:4])
item.append(struct)
item.append(name)
yield item
class AlignmentSeqTestCase(BalibaseTestCase):
def get_dataset_records(self):
"""Generator function to iterate over the record generator of each
unaligned fasta file.
"""
dataset_dir = os.path.join(self.balibase_path, "RV11.unaligned")
for filename in os.listdir(dataset_dir):
records = Bio.SeqIO.parse(
os.path.join(dataset_dir, filename),
"fasta")
yield records, filename
def assertSameResidues(self, str1, str2):
"""Strip strings of their '-' before comparing them
"""
return self.assertEqual(
str(str1).translate({ord('-'):None}),
str(str2).translate({ord('-'):None})
)
def test_simple_align(self):
"""Test alignments with the simplest metric.
As there can be a huge number of
solutions, we check only that we got the right score, and one valid
alignment.
"""
from alignementseq import align
score_fn = lambda a,b : -2 if a == '' or b == '' else -1 if a != b else 1
for s1, s2, filename in self.get_dataset_heads():
score, r1, r2 = align(s1, s2, score_fn)
(ex_r1, ex_r2, exp_score, *_) = Bio.pairwise2.align.globalms(
s1.seq, s2.seq, 1, -1, -2, -2, one_alignment_only=True)[0]
try:
self.assertSameResidues(r1.seq, s1.seq)
self.assertSameResidues(r2.seq, s2.seq)
self.assertEqual(score, sum(
-2 if a == '-' or b == '-' else
-1 if a != b else
1
for a,b in zip(r1.seq, r2.seq)))
self.assertEqual(score, exp_score)
except AssertionError:
print('from', filename, ':')
print(r1.seq)
print(r2.seq)
print('')
print(ex_r1)
print(ex_r2)
raise
def test_blosum_align(self):
"""Tests alignments with blosum but no gap extension.
"""
from alignementseq import align, vec_align
for s1, s2, filename in self.get_dataset_heads():
(ex_r1, ex_r2, exp_score, *_) = Bio.pairwise2.align.globalds(
s1.seq, s2.seq, blosum62, -8, -8, one_alignment_only=True)[0]
for method in align, vec_align:
score, r1, r2 = method(s1, s2)
try:
self.assertSameResidues(r1.seq, s1.seq)
self.assertSameResidues(r2.seq, s2.seq)
self.assertEqual(score, sum(
-8 if a == '-' or b == '-' else
blosum62[a,b] if (a,b) in blosum62 else
blosum62[b,a]
for a,b in zip(r1.seq, r2.seq)))
self.assertEqual(score, exp_score)
except AssertionError:
print('from', filename, "with", method, ":")
print(r1.seq)
print(r2.seq)
print('')
print(ex_r1)
print(ex_r2)
raise
def test_blosum_align2steps(self):
"""Tests alignments with blosum and gap extension.
"""
from alignementseq import align2steps
for s1, s2, filename in self.get_dataset_heads():
(ex_r1, ex_r2, exp_score, *_) = Bio.pairwise2.align.globaldd(
s1.seq, s2.seq, blosum62, -8, -4, -8, -4, one_alignment_only=True)[0]
score, r1, r2 = align2steps(s1, s2)
try:
self.assertSameResidues(r1.seq, s1.seq)
self.assertSameResidues(r2.seq, s2.seq)
calc_score = 0 # score calculated from r1 and r2
gap1, gap2 = False, False
for a,b in zip(r1.seq, r2.seq):
if a == '-':
if not gap1:
gap1 = True
gap2 = False # suppose 2 gaps are never aligned
calc_score -= 8
else:
calc_score -= 4
elif b == '-':
if not gap2:
gap2 = True
gap1 = False
calc_score -= 8
else:
calc_score -= 4
else:
gap1, gap2 = False, False
calc_score += blosum62[a,b] if (a,b) in blosum62 else blosum62[b,a]
self.assertEqual(score, calc_score)
self.assertEqual(score, exp_score)
except AssertionError:
print('from', filename, "with", align2steps, ":")
print(r1.seq)
print(r2.seq)
print('')
print(ex_r1)
print(ex_r2)
raise
def test_align_dihedrals(self):
for seq1, seq2, oseq1, oseq2, struct1, struct2, name in self.get_datasets_heads_with_struct():
skip = False
for seq, struct in ((oseq1, struct1), (oseq2, struct2)):
try:
chain = next(c for c in struct.get_chains() if
str(Bio.PDB.Polypeptide.Polypeptide(c).get_sequence()).startswith(str(seq.seq))
)
except StopIteration:
warnings.warn("No suitable chain found for seq id "+seq.id+" in structure "+struct.id+", skipping file.")
skip = True
break
polyp = Bio.PDB.Polypeptide.Polypeptide(chain)
if skip:
continue
# =============================================================================
# def test_multiple_align(self):
# """Tests the multiple_align function (using blosum and gap extension)."""
# #from alignementseq import multiple_align
# from Bio.Align.Applications import ClustalwCommandline
# from Bio import AlignIO
# import pip
#
# if not os.path.isfile("clustalo.py"):
# print("Fetching clustalo.py from Github...")
# urllib.request.urlretrieve(
# "https://raw.githubusercontent.com/ebi-wp/webservice-clients/master/python/clustalo.py",
# "clustalo.py")
# pip.main(["install --upgrade", "xmltramp2"])
# #pip("install --upgrade xmltramp2")
# print("Done")
# import clustalo
# # How to use: python clustalo.py --email <your@email.com> --sequence sp:wap_rat,sp:wap_mouse,sp:wap_pig
#
# for records, filename in self.get_dataset_records():
# clustalo("ariane.delrocq@polytechnique.edu", *list(records))
#
# print("Fine", filename)
# =============================================================================
def save_alignments(self, NameFile):
from alignementseq import align2steps
for s1, s2, filename in self.get_dataset_heads():
score, r1, r2 = align2steps(s1, s2)
with open("balibase/" + str(NameFile)+'.fasta', "w") as fd:
Bio.SeqIO.write((r1, r2), fd, "fasta")
class PerformanceTestCase(BalibaseTestCase):
"""Performance tests, slow.
Excluded from default test suite, run it with
``python -m unittest alignmentseq_tests.PerformanceTestCase``
"""
def setUp(self):
"""Loads titin sequences.
"""
super().setUp()
self.unit_timeout = int(os.environ.get("UNIT_TIMEOUT") or 60)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
self.titin_human, self.titin_mouse = Bio.SeqIO.parse(
Bio.Entrez.efetch(db="protein", id=["CAA62188","EDL27217"],
rettype="gp", retmode="text"),
"genbank")
def test_performance(self):
from alignementseq import align, vec_align
def biopython_align(seq1, seq2):
return Bio.pairwise2.align.globalds(
seq1.seq, seq2.seq, blosum62, -8, -8,
one_alignment_only=True)[0]
methods = (vec_align, align, biopython_align)
times = pd.DataFrame(columns=("length1", "length2", "method", "time"),
dtype=float)
for s1, s2, filename in self.get_dataset_heads():
for method in methods:
def to_time():
method(s1, s2)
t = timeit.Timer(to_time).timeit(1)
times.loc[len(times)] = (
len(s1.seq), len(s2.seq), method.__name__, t
)
times['length_product'] = times.length1 * times.length2
print(times)
ax = None
cmap = matplotlib.cm.inferno
colors = [ cmap(i/len(methods)) for i in range(len(methods)) ]
for im, method in enumerate(methods):
ax = times.loc[times.method == method.__name__].plot.scatter(
'length_product', 'time', c=colors[im],
label=method.__name__, ax=ax)
matplotlib.pyplot.savefig("timings.png")
def test_titin(self):
from alignementseq import align, vec_align
for method in vec_align, align:
def to_time():
method(self.titin_human, self.titin_mouse)
def run():
t = timeit.Timer(to_time).timeit(1)
print("{}: {}".format(method.__name__, t))
p = multiprocessing.Process(target=run)
p.start()
p.join(self.unit_timeout)
# Note: if the task eats up your memory, it can take a while for
# it to terminate if it times out.
if p.is_alive():
p.terminate()
p.join()
print("{}: timeout".format(method.__name__))
def load_tests(loader, standard_tests, pattern):
return unittest.defaultTestLoader.loadTestsFromTestCase(AlignmentSeqTestCase)
if __name__ == '__main__':
unittest.main(verbosity=2)