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|
#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2024 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyFinder package. #
# #
# MacSyFinder is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# MacSyFinder is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details . #
# #
# You should have received a copy of the GNU General Public License #
# along with MacSyFinder (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import os
import unittest
import shutil
import tempfile
import sysconfig
import argparse
from macsypy.profile import Profile
from macsypy.gene import CoreGene, ModelGene
from macsypy.model import Model
from macsypy.profile import ProfileFactory
from macsypy.config import Config, MacsyDefaults
from macsypy.registries import ModelLocation
from macsypy.error import MacsypyError
from tests import MacsyTest
class TestProfile(MacsyTest):
def setUp(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 50
self.cfg = Config(MacsyDefaults(), args)
if os.path.exists(self.cfg.working_dir()):
shutil.rmtree(self.cfg.working_dir())
os.makedirs(self.cfg.working_dir())
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except Exception:
pass
def test_len(self):
model = Model("functional/T12SS-simple-exch", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
###########################
# test compressed profile #
###########################
model = Model("functional_gzip/T12SS-simple-exch", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
model = Model("foo/compressed_profile", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
for ext in 'bz2', 'zip':
with self.subTest(ext=ext):
path = self.find_data('models', 'foo', 'profiles', f'{ext}.hmm.{ext}')
with self.catch_log(log_name='macsypy'):
with self.assertRaises(MacsypyError) as ctx:
Profile(gene, self.cfg, path)
self.assertEqual(str(ctx.exception),
f"Cannot read profile {path}: MacSyFinder does not support '{ext}' compression "
f"(only gzip).")
###################
# unreadable gzip #
###################
path = self.find_data('models', 'foo', 'profiles', 'bad_ext.hmm.gz')
with self.catch_log(log_name='macsypy'):
with self.assertRaises(MacsypyError) as ctx:
Profile(gene, self.cfg, path)
self.assertEqual(str(ctx.exception),
f"Cannot read profile {path}: Not a gzipped file (b'BZ')"
)
def test_ga_threshold(self):
# No GA threshold
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertFalse(profile.ga_threshold)
model = Model("foo/T2SS", 10)
# GA threshold line ends with ;
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertTrue(profile.ga_threshold)
# GA threshold line do NOT ends with ;
gene_name = 'PF05930.13'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertTrue(profile.ga_threshold)
# GA threshold invalid format string instead float
gene_name = 'bad_GA'
with self.catch_log(log_name='macsypy'):
# When a CoreGene is created a Profile is automatically instanciated
# So I mute the log to do not polute output
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
with self.catch_log(log_name='macsypy') as log:
profile = Profile(gene, self.cfg, path)
catch_msg = log.get_value().strip()
self.assertFalse(profile.ga_threshold)
self.assertEqual(catch_msg,
"bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.\n"
"GA score will not used for gene 'bad_GA'.")
# GA threshold invalid format only one score
gene_name = 'bad_GA_2'
with self.catch_log(log_name='macsypy'):
# When a CoreGene is created a Profile is automatically instanciated
# So I mute the log to do not polute output
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
with self.catch_log(log_name='macsypy') as log:
profile = Profile(gene, self.cfg, path)
catch_msg = log.get_value().strip()
self.assertFalse(profile.ga_threshold)
self.assertEqual(catch_msg,
"bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'.\n"
"GA score will not used for gene 'bad_GA_2'.")
def test_str(self):
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, path)
s = "{0} : {1}".format(gene.name, path)
self.assertEqual(str(profile), s)
#@unittest.skipIf(not shutil.which('hmmsearch'), 'hmmsearch not found in PATH')
@unittest.skip("For some reason this fails to find hmmer_results - skipping")
def test_execute_hmm_with_GA(self):
for db_type in ("gembase", "ordered_replicon", "unordered"):
self.cfg._set_db_type(db_type)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
# case GA threshold in profile
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, self.cfg, profile_path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(first_l.startswith("# hmmsearch :: search profile(s) against a sequence database"))
for _ in range(5):
# skip 4 lines
line = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(line.find(profile_path) != -1)
for _ in range(3):
# skip 2 lines
line = hmmer_raw_out_file.readline()
self.assertEqual("# model-specific thresholding: GA cutoffs", line.strip())
# test if profile is executed only once per run
report_bis = profile.execute()
self.assertIs(report, report_bis)
@unittest.skipIf(not shutil.which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_protected_path(self):
# create a hmmdir with space in name
self.cfg.hmmer_dir = lambda: 'hmmer results'
# create sequence_db path with space in path
seq_path = os.path.join(self.cfg.working_dir(), "test test1.fasta")
shutil.copyfile(self.find_data("base", "test_1.fasta"),
seq_path)
self.cfg._set_sequence_db(seq_path)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
# case GA threshold in profile
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, self.cfg, profile_path)
profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(first_l.startswith("# hmmsearch :: search profile(s) against a sequence database"))
for _ in range(5):
# skip 4 lines
line = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(line.find(profile_path) != -1)
for _ in range(3):
# skip 2 lines
line = hmmer_raw_out_file.readline()
self.assertEqual("# model-specific thresholding: GA cutoffs", line.strip())
@unittest.skipIf(not shutil.which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_w_GA_n_nocutga(self):
# case GA threshold in profile but --no-cut-ga is set
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 0
args.e_value_search = 0.5
args.no_cut_ga = True
cfg = Config(MacsyDefaults(), args)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, cfg, profile_path)
profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
for i in range(9):
line = hmmer_raw_out_file.readline()
self.assertEqual("# sequence reporting threshold: E-value <= 0.5", line.strip())
@unittest.skipIf(not shutil.which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_wo_GA(self):
# case cut-ga but no GA threshold in hmmprofile
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
# case -cut-ga and GA threshold in profile
profile_path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, profile_path)
with self.catch_log():
profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(first_l.startswith("# hmmsearch :: search profile(s) against a sequence database"))
for _ in range(5):
# skip 4 lines
line = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(line.find(profile_path) != -1)
for _ in range(3):
# skip 2 lines
line = hmmer_raw_out_file.readline()
self.assertEqual('# sequence reporting threshold: E-value <= 0.1', line.strip())
def test_execute_unknown_binary(self):
self.cfg._options['hmmer'] = "Nimportnaoik"
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc", )
profile = Profile(gene, self.cfg, path)
with self.catch_log():
with self.assertRaises(RuntimeError):
profile.execute()
def test_execute_hmmer_failed(self):
fake_hmmer = os.path.join(tempfile.gettempdir(), 'hmmer_failed')
with open(fake_hmmer, 'w') as hmmer:
hmmer.write("""#! {}
import sys
sys.exit(127)
""".format(sysconfig.sys.executable))
try:
os.chmod(hmmer.name, 0o755)
self.cfg._options['hmmer'] = hmmer.name
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc", )
profile = Profile(gene, self.cfg, path)
with self.catch_log():
with self.assertRaisesRegex(RuntimeError,
"an error occurred during Hmmer "
"execution: command = .* : return code = 127 .*"):
profile.execute()
finally:
try:
os.unlink(fake_hmmer)
except Exception:
pass
|
