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|
# Copyright 2008-2011 by Peter Cock. All rights reserved.
# Revisions copyright 2012 by Christian Brueffer. 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.
"""Tests for ClustalOmega tool."""
import os
import unittest
import warnings
from subprocess import getoutput
from Bio import Align
from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError
from Bio import SeqIO
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
from Bio.Align.Applications import ClustalOmegaCommandline
from Bio.Application import ApplicationError
#################################################################
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
clustalo_exe = None
try:
output = getoutput("clustalo --help")
if output.startswith("Clustal Omega"):
clustalo_exe = "clustalo"
except FileNotFoundError:
pass
if not clustalo_exe:
raise MissingExternalDependencyError(
"Install clustalo if you want to use Clustal Omega from Biopython."
)
class ClustalOmegaTestCase(unittest.TestCase):
def setUp(self):
self.files_to_clean = set()
def tearDown(self):
for filename in self.files_to_clean:
if os.path.isfile(filename):
os.remove(filename)
def standard_test_procedure(self, cline):
"""Shared test procedure used by all tests."""
# Overwrite existing files.
cline.force = True
# Mark output files for later cleanup.
self.add_file_to_clean(cline.outfile)
if cline.guidetree_out:
self.add_file_to_clean(cline.guidetree_out)
input_records = SeqIO.to_dict(SeqIO.parse(cline.infile, "fasta"))
self.assertEqual(str(eval(repr(cline))), str(cline))
output, error = cline()
self.assertTrue(not output or output.strip().startswith("CLUSTAL"))
# Test if ClustalOmega executed successfully.
self.assertTrue(
error.strip() == ""
or error.startswith(
(
"WARNING: Sequence type is DNA.",
"WARNING: DNA alignment is still experimental.",
)
)
)
# TODO - Try and parse this with Bio.Nexus?
if cline.guidetree_out:
self.assertTrue(os.path.isfile(cline.guidetree_out))
def add_file_to_clean(self, filename):
"""Add a file for deferred removal by the tearDown routine."""
self.files_to_clean.add(filename)
#################################################################
class ClustalOmegaTestErrorConditions(ClustalOmegaTestCase):
def test_empty_file(self):
"""Test an empty file."""
input_file = "does_not_exist.fasta"
self.assertFalse(os.path.isfile(input_file))
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
try:
stdout, stderr = cline()
except ApplicationError as err:
message = str(err)
self.assertTrue(
"Cannot open sequence file" in message
or "Cannot open input file" in message
or "Non-zero return code" in message,
message,
)
else:
self.fail(f"Should have failed, returned:\n{stdout}\n{stderr}")
def test_single_sequence(self):
"""Test an input file containing a single sequence."""
input_file = "Fasta/f001"
self.assertTrue(os.path.isfile(input_file))
self.assertEqual(len(list(SeqIO.parse(input_file, "fasta"))), 1)
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
try:
stdout, stderr = cline()
except ApplicationError as err:
self.assertIn("contains 1 sequence, nothing to align", str(err))
else:
self.fail(f"Should have failed, returned:\n{stdout}\n{stderr}")
def test_invalid_format(self):
"""Test an input file in an invalid format."""
input_file = "Medline/pubmed_result1.txt"
self.assertTrue(os.path.isfile(input_file))
cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file)
with self.assertRaises(ApplicationError) as cm:
stdout, stderr = cline()
self.fail(f"Should have failed, returned:\n{stdout}\n{stderr}")
err = str(cm.exception)
# Ideally we'd catch the return code and raise the specific
# error for "invalid format".
self.assertIn("Can't determine format of sequence file", err)
#################################################################
class ClustalOmegaTestNormalConditions(ClustalOmegaTestCase):
def test_simple_fasta(self):
"""Test a simple fasta file."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
cline = ClustalOmegaCommandline(
clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal"
)
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(
str(alignment),
"""\
gi|134891 0 GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAGGCACCTAACATCCATTCACA
0 ---------..-........|......|....|......|..............|.----
gi|129628 0 ---------MP-VVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDPNRSLTI----
gi|134891 60 CCCAACACAGGCCAGCGACTTCTGGGGCTCAGCCACAGACATGGTTTGTNACTNTTGAGC
60 -----.|.||.......|....|-------------------......|.......||..
gi|129628 46 -----WANAGEVPENITALSDVT-------------------ESSIVKTIKQHDVDGAVV
gi|134891 120 TTCTGTTCCTAGAGAATCCTAGAGGCTTGATTGGCCCAGGCTGCTGTNTGTNCTGGAGG-
120 ...--------..|.|......|..............|...|..............|..-
gi|129628 82 IVD--------LEGVASRMVSRAISQADLVLIPMRPKALDATIGAQSLQLIAEEEEAIDR
gi|134891 179 -CAAAGAATCCCTACCTCCTAGGGGTGAAAGGAAATNAAAATGGAAAGTTCTTGTAGCGC
180 -.|.|...|....|.......|........|------------...........||....
gi|129628 134 KIAHAVVFTMVSPAIRSHEYTGIKASLIENG------------VEIIEPPLVERTAYSAL
gi|134891 238 AAGGCCTGACATGGGTAGCTGCTCAATAAATGCTAGTNTGTTATTTC 285
240 ...|..........|..........|.|-----.|.....|.|..-- 287
gi|129628 182 FQFGGNLHSMKSKQGNMAAAIENAEAFA-----MAIFKKLTEALR-- 222
""",
)
self.assertEqual(
alignment.column_annotations["clustal_consensus"],
" * * * * * * ** * * * ** * * * * * * * * * * * * ** * * * * * * * ",
)
def test_properties(self):
"""Test setting options via properties."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
cline = ClustalOmegaCommandline(clustalo_exe)
cline.infile = input_file
cline.outfile = output_file
cline.outfmt = "clustal"
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(
str(alignment),
"""\
gi|134891 0 GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAGGCACCTAACATCCATTCACA
0 ---------..-........|......|....|......|..............|.----
gi|129628 0 ---------MP-VVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDPNRSLTI----
gi|134891 60 CCCAACACAGGCCAGCGACTTCTGGGGCTCAGCCACAGACATGGTTTGTNACTNTTGAGC
60 -----.|.||.......|....|-------------------......|.......||..
gi|129628 46 -----WANAGEVPENITALSDVT-------------------ESSIVKTIKQHDVDGAVV
gi|134891 120 TTCTGTTCCTAGAGAATCCTAGAGGCTTGATTGGCCCAGGCTGCTGTNTGTNCTGGAGG-
120 ...--------..|.|......|..............|...|..............|..-
gi|129628 82 IVD--------LEGVASRMVSRAISQADLVLIPMRPKALDATIGAQSLQLIAEEEEAIDR
gi|134891 179 -CAAAGAATCCCTACCTCCTAGGGGTGAAAGGAAATNAAAATGGAAAGTTCTTGTAGCGC
180 -.|.|...|....|.......|........|------------...........||....
gi|129628 134 KIAHAVVFTMVSPAIRSHEYTGIKASLIENG------------VEIIEPPLVERTAYSAL
gi|134891 238 AAGGCCTGACATGGGTAGCTGCTCAATAAATGCTAGTNTGTTATTTC 285
240 ...|..........|..........|.|-----.|.....|.|..-- 287
gi|129628 182 FQFGGNLHSMKSKQGNMAAAIENAEAFA-----MAIFKKLTEALR-- 222
""",
)
self.assertEqual(
alignment.column_annotations["clustal_consensus"],
" * * * * * * ** * * * ** * * * * * * * * * * * * ** * * * * * * * ",
)
def test_input_filename_with_space(self):
"""Test an input filename containing a space."""
input_file = "Clustalw/temp horses.fasta"
with open(input_file, "w") as handle:
SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle, "fasta")
output_file = "temp_test.aln"
cline = ClustalOmegaCommandline(
clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal"
)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(
str(alignment),
"""\
A 0 -CACACACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA 40
B 0 -CACACAACAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA 40
C 0 -CACAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA 40
D 0 -CAACAAAACAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA 40
E 0 -CAACAAAAACAAAAAAAACAAAAAAAAAAAAAAAAAAAAA 40
F 0 ACAAAAAAAACACACAAAACAAAAAAAAAAAAAAAAAAAA- 40
G 0 ACAAAAAAAACACAACAAACAAAAAAAAAAAAAAAAAAAA- 40
H 0 ACAAAAAAAACAACAAAAACAAAAAAAAAAAAAAAAAAAA- 40
I 0 ACAAAAAAAAACAAAACAACAAAAAAAAAAAAAAAAAAAA- 40
J 0 ACAAAAAAAAACAAAAACACAAAAAAAAAAAAAAAAAAAA- 40
""",
)
self.assertEqual(
alignment.column_annotations["clustal_consensus"],
" ** ********************** ",
)
def test_output_filename_with_spaces(self):
"""Test an output filename containing spaces."""
input_file = "Registry/seqs.fasta"
output_file = "temp with spaces.aln"
cline = ClustalOmegaCommandline(
clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal"
)
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(
str(alignment),
"""\
gi|134891 0 GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAGGCACCTAACATCCATTCACA
0 ---------..-........|......|....|......|..............|.----
gi|129628 0 ---------MP-VVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDPNRSLTI----
gi|134891 60 CCCAACACAGGCCAGCGACTTCTGGGGCTCAGCCACAGACATGGTTTGTNACTNTTGAGC
60 -----.|.||.......|....|-------------------......|.......||..
gi|129628 46 -----WANAGEVPENITALSDVT-------------------ESSIVKTIKQHDVDGAVV
gi|134891 120 TTCTGTTCCTAGAGAATCCTAGAGGCTTGATTGGCCCAGGCTGCTGTNTGTNCTGGAGG-
120 ...--------..|.|......|..............|...|..............|..-
gi|129628 82 IVD--------LEGVASRMVSRAISQADLVLIPMRPKALDATIGAQSLQLIAEEEEAIDR
gi|134891 179 -CAAAGAATCCCTACCTCCTAGGGGTGAAAGGAAATNAAAATGGAAAGTTCTTGTAGCGC
180 -.|.|...|....|.......|........|------------...........||....
gi|129628 134 KIAHAVVFTMVSPAIRSHEYTGIKASLIENG------------VEIIEPPLVERTAYSAL
gi|134891 238 AAGGCCTGACATGGGTAGCTGCTCAATAAATGCTAGTNTGTTATTTC 285
240 ...|..........|..........|.|-----.|.....|.|..-- 287
gi|129628 182 FQFGGNLHSMKSKQGNMAAAIENAEAFA-----MAIFKKLTEALR-- 222
""",
)
self.assertEqual(
alignment.column_annotations["clustal_consensus"],
" * * * * * * ** * * * ** * * * * * * * * * * * * ** * * * * * * * ",
)
def test_large_fasta_file(self):
"""Test a large fasta input file."""
# Create a large input file by converting another example file
# (See Bug 2804, this will produce so much output on stdout that
# subprocess could suffer a deadlock and hang). Using all the
# records should show the deadlock but is very slow - just thirty
# seems to lockup on Mac OS X, even 20 on Linux (without the fix).
input_file = "temp_cw_prot.fasta"
records = list(SeqIO.parse("NBRF/Cw_prot.pir", "pir"))[:40]
with open(input_file, "w") as handle:
SeqIO.write(records, handle, "fasta")
del handle, records
output_file = "temp_cw_prot.aln"
cline = ClustalOmegaCommandline(
clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal"
)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
def test_newtree_files(self):
"""Test requesting a guide tree."""
input_file = "Fasta/f002"
output_file = "temp_test.aln"
newtree_file = "temp_test.dnd"
alignment_text = """\
gi|134891 0 CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATGTGATTGANATNATGACTCTA
gi|134891 0 ---------CGGAGCCAGCGAGCATAT---------------------------------
gi|159293 0 ------------------------------------------------------------
gi|134891 60 CTCCTAAAAGGGAAAAANCAATATCCTTGTTTACAGAAGAGAAACAAACAAGCCCCACTC
gi|134891 18 ----------------------------------------------------GCTGCATG
gi|159293 0 --------------------------------------------GATCAAATCTGCACTG
gi|134891 120 AGCTCAGTCACAGGAGAGANCACAGAAAGTCTTAGGATCATGANCTCTGAA-AAAAAGAG
gi|134891 26 -------------------------AGGACCTTTCTATCTTACATTATGGC-TGGGAATC
gi|159293 16 TGTCTACATATAGGAAAGGTCCTGGTGTGTGCTAATGTTCCCAATGCAGGACTTGAGGAA
gi|134891 179 AAACCTTATCTTTNCTTTGTGGTTCCTTTAAACACACTCACACACACTTGGTCAGAGATG
gi|134891 60 TTACTCTTTCATCTG-------ATACCTTGTTCAGATTTCAAAATAGTTGTAGCCTTATC
gi|159293 76 GAGCTCTGTTATATGTTTCCATTTCTCTTTATCAAAGATAACCAAACCTTATGGCCCTT-
gi|134891 239 CTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGC----------AGAGGGAC
gi|134891 113 CTGGTTTTACAGATGTGAAACTT----TCAAGAGATTTACTGACTTTCCTAGAATA----
gi|159293 135 ---ATAACAATGGAGGCACTGGCTGCCTCTTAATTTTCAATCATGGACCTAAAGAAGTAC
gi|134891 289 GTTTGA--GTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTT
gi|134891 165 --------GT--------------TTCTCTACTGGAAACCTGATGCTTTTATAAGCCATT
gi|159293 192 TCTGAAGGGTCTCAACAATGCCAGGTGGGGACAGATATACTCAGAGATTATCCAGGTCTG
gi|134891 347 ATGTNAAGCNTGACAACACCAGGCAGGTATGAGAGGA-AAGCAAGGCCCGTCCATNGCTG
gi|134891 203 GTGATTAGGATGACTGTTACAGGCTTAGCTTTGTGTGAAANCCAGTCACCTTT------C
gi|159293 252 CCTCCCAGCGAGCC-----------TGGA------GT-ACACCAGACCCTCCTAGAGAAA
gi|134891 406 TCCGTACNCTTACGGNTTGCTTGTNGGAGNCATTTNGGTATTGTTTGTTGTAANANCCAA
gi|134891 257 TCCTAGGTAATGAGTAGTGCTGTTCATATTACTNT-------AAGTTCTATAGCATACTT
gi|159293 294 TCTGTT------------------------------------ATAATTTACCACCCACTT
gi|134891 466 AANGGGCTTTGGNNTGGNAAAA----GGGCAGANNGGGGGGGTTGGTGTNGTTTTTTGG-
gi|134891 310 GCNATCCTTTANCCATGCTTATCATANGTACCATTTGAGGAATTGNTT-----TGCCCTT
gi|159293 318 ATCCACCTTTAAACTTGGGGAA----GGNNGCN------TTTCAAATTAAATTTAATCNT
gi|134891 521 GGGGANNNTTTNGATTTGG-------TNCCGGGNTTTNGTTTNCCNCGGNACCGGNTTTT
gi|134891 365 TTG-GGTTTNTTNTTGGTAA--ANNNTTCCCGGGTGGGGGNGGTNNNGAAA---------
gi|159293 368 NGGGGGNTTTTAAACTTTAACCCTTTTNCCNTTNTNGGGGTNGGNANTTGNCCCCNTTAA
gi|134891 574 GGTTGGGGNCCATTTNTGNGGGGCNTTGGNGTTNCNTTNCCCNNNTNNGANTGGTTTNA
gi|134891 413 -----------------------------------------------------------
gi|159293 428 AGGGGGNNCCCCT-NCNNGGGGGAATAA-AACAA----------NTTNNTTT--TTT--
gi|134891 633
gi|134891 413
gi|159293 471
"""
clustal_consensus = " * * * * * * * * * ** ** * * * * * * * * * * * ** * * * * * * * ** * * * * ** * * ** * * **** * * * * * * * * * ** * * "
cline = ClustalOmegaCommandline(
clustalo_exe,
infile=input_file,
outfile=output_file,
guidetree_out=newtree_file,
outfmt="clustal",
)
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(str(alignment), alignment_text)
self.assertEqual(
alignment.column_annotations["clustal_consensus"], clustal_consensus
)
cline.guidetree_out = "temp with space.dnd"
self.standard_test_procedure(cline)
alignment = Align.read(cline.outfile, "clustal")
self.assertEqual(str(alignment), alignment_text)
self.assertEqual(
alignment.column_annotations["clustal_consensus"], clustal_consensus
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
