def test_find_attc_max_linear(self):
integrase = pd.DataFrame(
{
'pos_beg': 1545830,
'pos_end': 1546807,
'strand': -1,
'evalue': 1.100000e-21,
'type_elt': 'protein',
'annotation': 'intI',
'model': 'intersection_tyr_intI',
'distance_2attC': np.nan
},
index=['OBAL001.B.00005.C001_141'],
columns=self.columns)
integrase = integrase.astype(dtype=self.dtype)
self.integron.integrase = integrase
attC = pd.DataFrame(
{
'pos_beg': [1547800, 1548775],
'pos_end': [1547859, 1548834],
'strand': [1, 1],
'evalue': [0.00049, 0.00009],
'type_elt': ['attC', 'attC'],
'annotation': ['attC', 'attC'],
'model': ['attc_4', 'attc_4'],
'distance_2attC': [np.nan, 916.0]
},
index=['attc_001', 'attc_002'],
columns=self.columns)
attC = attC.astype(dtype=self.dtype)
self.integron.attC = attC
integrons = [self.integron]
max_final = find_attc_max(integrons,
self.replicon,
self.cfg.distance_threshold,
self.cfg.model_attc_path,
self.cfg.max_attc_size,
self.cfg.min_attc_size,
circular=False,
out_dir=self.tmp_dir)
exp = pd.DataFrame(
{
'Accession_number':
['OBAL001.B.00005.C001', 'OBAL001.B.00005.C001'],
'cm_attC': ['attC_4', 'attC_4'],
'cm_debut': [4, 1],
'cm_fin': [44, 47],
'pos_beg': [1547800, 1548775],
'pos_end': [1547859, 1548834],
'sens': ['+', '+'],
'evalue': [0.000240, 0.000045]
},
index=[0, 1],
columns=self.max_cols)
exp = exp.astype(dtype=self.max_dtype)
pdt.assert_frame_equal(max_final, exp)
def test_find_attc_max_In0(self):
replicon_name = 'ESCO001.B.00018.P002'
replicon_path = self.find_data(os.path.join('Replicons', replicon_name + '.fst'))
topologies = Topology('circ')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
integron = Integron(replicon, self.cfg)
integrase = pd.DataFrame({'pos_beg': [90229],
'pos_end': [91242],
'strand': -1,
'evalue': 1.400000e-24,
'type_elt': 'protein',
'annotation': 'intI',
'model': 'intersection_tyr_intI',
'distance_2attC': np.nan
},
index=['ESCO001.B.00018.P002_106'],
columns=self.columns)
integrase = integrase.astype(dtype=self.dtype)
integron.integrase = integrase
integrons = [integron]
max_final = find_attc_max(integrons, replicon,
self.cfg.distance_threshold, self.cfg.model_attc_path,
self.cfg.max_attc_size, self.cfg.min_attc_size,
circular=True,
out_dir=self.tmp_dir)
exp = pd.DataFrame(columns=self.max_cols)
exp = exp.astype(dtype=self.max_dtype)
pdt.assert_frame_equal(max_final, exp)
def test_find_attc_max_linear(self):
integrase = pd.DataFrame({'pos_beg': 1545830,
'pos_end': 1546807,
'strand': -1,
'evalue': 1.100000e-21,
'type_elt': 'protein',
'annotation': 'intI',
'model': 'intersection_tyr_intI',
'distance_2attC': np.nan
},
index=['OBAL001.B.00005.C001_141'],
columns=self.columns)
integrase = integrase.astype(dtype=self.dtype)
self.integron.integrase = integrase
attC = pd.DataFrame({'pos_beg': [1547800, 1548775],
'pos_end': [1547859, 1548834],
'strand': [1, 1],
'evalue': [0.00049, 0.00009],
'type_elt': ['attC', 'attC'],
'annotation': ['attC', 'attC'],
'model': ['attc_4', 'attc_4'],
'distance_2attC': [np.nan, 916.0]
},
index=['attc_001', 'attc_002'],
columns=self.columns)
attC = attC.astype(dtype=self.dtype)
self.integron.attC = attC
integrons = [self.integron]
max_final = find_attc_max(integrons, self.replicon,
self.cfg.distance_threshold, self.cfg.model_attc_path,
self.cfg.max_attc_size, self.cfg.min_attc_size,
circular=False,
out_dir=self.tmp_dir)
exp = pd.DataFrame({'Accession_number': ['OBAL001.B.00005.C001', 'OBAL001.B.00005.C001'],
'cm_attC': ['attC_4', 'attC_4'],
'cm_debut': [4, 1],
'cm_fin': [44, 47],
'pos_beg': [1547800, 1548775],
'pos_end': [1547859, 1548834],
'sens': ['+', '+'],
'evalue': [0.000240, 0.000045]
},
index=[0, 1],
columns=self.max_cols
)
exp = exp.astype(dtype=self.max_dtype)
pdt.assert_frame_equal(max_final, exp)
def test_find_attc_max_calin(self):
attC = pd.DataFrame(
{
'pos_beg': [421689],
'pos_end': [421764],
'strand': [1],
'evalue': [0.13],
'type_elt': ['attC'],
'annotation': ['attC'],
'model': ['attc_4'],
'distance_2attC': [np.nan]
},
index=['attc_001'],
columns=self.columns)
attC = attC.astype(dtype=self.dtype)
self.integron.attC = attC
integrons = [self.integron]
max_final = find_attc_max(integrons,
self.replicon,
self.cfg.distance_threshold,
self.cfg.model_attc_path,
self.cfg.max_attc_size,
self.cfg.min_attc_size,
circular=True,
out_dir=self.tmp_dir)
exp = pd.DataFrame(
{
'Accession_number': ['OBAL001.B.00005.C001'],
'cm_attC': ['attC_4'],
'cm_debut': [1],
'cm_fin': [47],
'pos_beg': [421689],
'pos_end': [421764],
'sens': ['+'],
'evalue': [0.062]
},
index=[0],
columns=self.max_cols)
exp = exp.astype(dtype=self.max_dtype)
pdt.assert_frame_equal(max_final, exp)
def test_find_attc_max_calin(self):
attC = pd.DataFrame({'pos_beg': [421689],
'pos_end': [421764],
'strand': [1],
'evalue': [0.13],
'type_elt': ['attC'],
'annotation': ['attC'],
'model': ['attc_4'],
'distance_2attC': [np.nan]
},
index=['attc_001'],
columns=self.columns)
attC = attC.astype(dtype=self.dtype)
self.integron.attC = attC
integrons = [self.integron]
max_final = find_attc_max(integrons, self.replicon,
self.cfg.distance_threshold, self.cfg.model_attc_path,
self.cfg.max_attc_size, self.cfg.min_attc_size,
circular=True,
out_dir=self.tmp_dir)
exp = pd.DataFrame({'Accession_number': ['OBAL001.B.00005.C001'],
'cm_attC': ['attC_4'],
'cm_debut': [1],
'cm_fin': [47],
'pos_beg': [421689],
'pos_end': [421764],
'sens': ['+'],
'evalue': [0.062]
},
index=[0],
columns=self.max_cols
)
exp = exp.astype(dtype=self.max_dtype)
pdt.assert_frame_equal(max_final, exp)
def find_integron_in_one_replicon(replicon, config):
"""
scan replicon for integron.
* presence of integrase
* presence of attC sites
* presence of promoters and attI sites
depending on the configuration
* perform functional annotation
produce a file containing presence of putative integrons
depending on configuration
* produce genbank file with replicon and annotations with integrons
* produce schema of replicon with integrons (in pdf)
:param replicon: the replicon to analyse.
:type replicon: a :class:`Bio.SeqRecord` object.
:param config: The configuration
:type config: a :class:`integron_finder.config.Config` object.
:returns: the path to the integron file (<replicon_id>.integrons)
and the summary file (<replicon_id.summary>).
if there is no integron the summary file is None
:rtype: tuple (str integron_file, str summary_file) or (str integron_file, None)
"""
result_tmp_dir = config.tmp_dir(replicon.id)
try:
os.mkdir(result_tmp_dir)
except OSError:
pass
tmp_replicon_path = os.path.join(result_tmp_dir, replicon.id + '.fst')
SeqIO.write(replicon, tmp_replicon_path, "fasta")
# create attr path
# used to generate protein file with prodigal
replicon.path = tmp_replicon_path
# func_annot_path is the canonical path for Functional_annotation
# path_func_annot is the path provide on the command line
if config.func_annot and not config.no_proteins and not config.path_func_annot:
if os.path.exists('bank_hmm'):
fa_hmm = scan_hmm_bank('bank_hmm')
elif os.path.exists(config.func_annot_path):
fa_hmm = scan_hmm_bank(config.func_annot_path)
else:
raise IntegronError("the dir '{}' neither 'bank_hmm' exists, specify the location of hmm "
"profile with --path-func-annot option".format(config.func_annot_path))
is_func_annot = True
elif config.path_func_annot and config.no_proteins is False:
fa_hmm = scan_hmm_bank(config.path_func_annot)
is_func_annot = True
else:
is_func_annot = False
if is_func_annot and not fa_hmm:
_log.warning("No hmm profiles for functional annotation detected, skip functional annotation step.")
if config.gembase_path:
protein_db = GembaseDB(replicon, config, gembase_path=config.gembase_path)
elif config.gembase:
protein_db = GembaseDB(replicon, config)
else:
protein_db = ProdigalDB(replicon, config)
##################
# Default search #
##################
intI_file = os.path.join(result_tmp_dir, replicon.id + "_intI.res")
phageI_file = os.path.join(result_tmp_dir, replicon.id + "_phage_int.res")
attC_default_file = os.path.join(result_tmp_dir, replicon.id + "_attc_table.res")
try:
if not config.no_proteins:
if not os.path.isfile(intI_file) or not os.path.isfile(phageI_file):
find_integrase(replicon.id, protein_db.protfile, result_tmp_dir, config)
_log.info("Starting Default search ... :")
if not os.path.isfile(attC_default_file):
# find attc with cmsearch
find_attc(tmp_replicon_path, replicon.name, config.cmsearch, result_tmp_dir, config.model_attc_path,
incE=config.evalue_attc,
cpu=config.cpu)
_log.info("Default search done... : ")
integrons = find_integron(replicon, protein_db, attC_default_file, intI_file, phageI_file, config)
#########################
# Search with local_max #
#########################
if config.local_max:
_log.info("Starting search with local_max...:")
if not os.path.isfile(os.path.join(result_tmp_dir, "integron_max.pickle")):
circular = True if replicon.topology == 'circ' else False
integron_max = find_attc_max(integrons, replicon, config.distance_threshold,
config.model_attc_path,
max_attc_size=config.max_attc_size,
min_attc_size=config.min_attc_size,
circular=circular, out_dir=result_tmp_dir,
cpu=config.cpu,
evalue_attc=config.evalue_attc)
integron_max.to_pickle(os.path.join(result_tmp_dir, "integron_max.pickle"))
_log.info("Search with local_max done... :")
else:
integron_max = pd.read_pickle(os.path.join(result_tmp_dir, "integron_max.pickle"))
integron_max = integron_max[(integron_max.evalue < config.evalue_attc) &
(abs(integron_max.pos_end - integron_max.pos_beg) < config.max_attc_size) &
(config.min_attc_size < abs(integron_max.pos_end - integron_max.pos_beg))]
_log.info("Search with local_max was already done, continue... :")
integrons = find_integron(replicon, protein_db, integron_max, intI_file, phageI_file, config)
##########################
# Add promoters and attI #
##########################
for integron in integrons:
integron_type = integron.type()
if integron_type != "In0": # complete & CALIN
if not config.no_proteins:
_log.info("Adding proteins ... :")
integron.add_proteins(protein_db)
if config.promoter_attI:
_log.info("Adding promoters and attI ... :")
if integron_type == "complete":
integron.add_promoter()
integron.add_attI()
elif integron_type == "In0":
integron.add_attI()
integron.add_promoter()
#########################
# Functional annotation #
#########################
if is_func_annot and fa_hmm:
_log.info("Starting functional annotation ...:")
func_annot(integrons, replicon, protein_db, fa_hmm, config, result_tmp_dir)
#######################
# Writing out results #
#######################
_log.info("Writing out results for replicon {}".format(replicon.id))
if config.pdf:
for j, integron in enumerate(integrons, 1):
if integron.type() == "complete":
integron.draw_integron(file=os.path.join(config.result_dir, "{}_{}.pdf".format(replicon.id, j)))
base_outfile = os.path.join(config.result_dir, replicon.id)
integron_file = base_outfile + ".integrons"
_log.debug("Writing integron_file {}".format(integron_file))
if integrons:
integrons_report = results.integrons_report(integrons)
integrons_report.to_csv(integron_file, sep="\t", index=False, na_rep="NA")
summary = results.summary(integrons_report)
summary_file = base_outfile + ".summary"
summary.to_csv(summary_file, sep="\t", na_rep="NA", index=False,
columns=['ID_replicon', 'ID_integron', 'complete', 'In0', 'CALIN'])
if config.gbk:
add_feature(replicon, integrons_report, protein_db, config.distance_threshold)
SeqIO.write(replicon, os.path.join(config.result_dir, replicon.id + ".gbk"), "genbank")
else:
with open(integron_file, "w") as out_f:
out_f.write("# No Integron found\n")
summary_file = None
except integron_finder.EmptyFileError as err:
_log.warning('############ Skip replicon {} ############'.format(replicon.name))
integron_file = ''
summary_file = ''
#########################
# clean temporary files #
#########################
if not config.keep_tmp:
try:
shutil.rmtree(result_tmp_dir)
except Exception as err:
_log.warning("Cannot remove temporary results : '{} : {}'".format(result_tmp_dir, str(err)))
return integron_file, summary_file
def find_integron_in_one_replicon(replicon, config):
"""
scan replicon for integron.
* presence of integrase
* presence of attC sites
* presence of promoters and attI sites
depending on the configuration
* perform functional annotation
produce a file containing presence of putative integrons
depending on configuration
* produce genbank file with replicon and annotations with integrons
* produce schema of replicon with integrons (in pdf)
:param replicon: the replicon to analyse.
:type replicon: a :class:`Bio.SeqRecord` object.
:param config: The configuration
:type config: a :class:`integron_finder.config.Config` object.
:returns: the path to the integron file (<replicon_id>.integrons)
and the summary file (<replicon_id.summary>).
if there is no integron the summary file is None
:rtype: tuple (str integron_file, str summary_file) or (str integron_file, None)
"""
result_tmp_dir = config.tmp_dir(replicon.id)
try:
os.mkdir(result_tmp_dir)
except OSError:
pass
tmp_replicon_path = os.path.join(result_tmp_dir, replicon.id + '.fst')
SeqIO.write(replicon, tmp_replicon_path, "fasta")
# create attr path
# used to generate protein file with prodigal
replicon.path = tmp_replicon_path
# func_annot_path is the canonical path for Functional_annotation
# path_func_annot is the path provide on the command line
if config.func_annot and not config.no_proteins and not config.path_func_annot:
if os.path.exists('bank_hmm'):
fa_hmm = scan_hmm_bank('bank_hmm')
elif os.path.exists(config.func_annot_path):
fa_hmm = scan_hmm_bank(config.func_annot_path)
else:
raise IntegronError(
"the dir '{}' neither 'bank_hmm' exists, specify the location of hmm "
"profile with --path-func-annot option".format(
config.func_annot_path))
is_func_annot = True
elif config.path_func_annot and config.no_proteins is False:
fa_hmm = scan_hmm_bank(config.path_func_annot)
is_func_annot = True
else:
is_func_annot = False
if is_func_annot and not fa_hmm:
_log.warning(
"No hmm profiles for functional annotation detected, skip functional annotation step."
)
if config.gembase_path:
protein_db = GembaseDB(replicon,
config,
gembase_path=config.gembase_path)
elif config.gembase:
protein_db = GembaseDB(replicon, config)
else:
protein_db = ProdigalDB(replicon, config)
##################
# Default search #
##################
intI_file = os.path.join(result_tmp_dir, replicon.id + "_intI.res")
phageI_file = os.path.join(result_tmp_dir, replicon.id + "_phage_int.res")
attC_default_file = os.path.join(result_tmp_dir,
replicon.id + "_attc_table.res")
try:
if not config.no_proteins:
if not os.path.isfile(intI_file) or not os.path.isfile(
phageI_file):
find_integrase(replicon.id, protein_db.protfile,
result_tmp_dir, config)
_log.info("Starting Default search ... :")
if not os.path.isfile(attC_default_file):
# find attc with cmsearch
find_attc(tmp_replicon_path,
replicon.name,
config.cmsearch,
result_tmp_dir,
config.model_attc_path,
incE=config.evalue_attc,
cpu=config.cpu)
_log.info("Default search done... : ")
integrons = find_integron(replicon, protein_db, attC_default_file,
intI_file, phageI_file, config)
#########################
# Search with local_max #
#########################
if config.local_max:
_log.info("Starting search with local_max...:")
if not os.path.isfile(
os.path.join(result_tmp_dir, "integron_max.pickle")):
circular = True if replicon.topology == 'circ' else False
integron_max = find_attc_max(
integrons,
replicon,
config.distance_threshold,
config.model_attc_path,
max_attc_size=config.max_attc_size,
min_attc_size=config.min_attc_size,
circular=circular,
out_dir=result_tmp_dir,
cpu=config.cpu,
evalue_attc=config.evalue_attc)
integron_max.to_pickle(
os.path.join(result_tmp_dir, "integron_max.pickle"))
_log.info("Search with local_max done... :")
else:
integron_max = pd.read_pickle(
os.path.join(result_tmp_dir, "integron_max.pickle"))
integron_max = integron_max[
(integron_max.evalue < config.evalue_attc)
& (abs(integron_max.pos_end -
integron_max.pos_beg) < config.max_attc_size) &
(config.min_attc_size <
abs(integron_max.pos_end - integron_max.pos_beg))]
_log.info(
"Search with local_max was already done, continue... :")
integrons = find_integron(replicon, protein_db, integron_max,
intI_file, phageI_file, config)
##########################
# Add promoters and attI #
##########################
for integron in integrons:
integron_type = integron.type()
if integron_type != "In0": # complete & CALIN
if not config.no_proteins:
_log.info("Adding proteins ... :")
integron.add_proteins(protein_db)
if config.promoter_attI:
_log.info("Adding promoters and attI ... :")
if integron_type == "complete":
integron.add_promoter()
integron.add_attI()
elif integron_type == "In0":
integron.add_attI()
integron.add_promoter()
#########################
# Functional annotation #
#########################
if is_func_annot and fa_hmm:
_log.info("Starting functional annotation ...:")
func_annot(integrons, replicon, protein_db, fa_hmm, config,
result_tmp_dir)
#######################
# Writing out results #
#######################
_log.info("Writing out results for replicon {}".format(replicon.id))
if config.pdf:
for j, integron in enumerate(integrons, 1):
if integron.type() == "complete":
integron.draw_integron(file=os.path.join(
config.result_dir, "{}_{}.pdf".format(replicon.id, j)))
base_outfile = os.path.join(config.result_dir, replicon.id)
integron_file = base_outfile + ".integrons"
_log.debug("Writing integron_file {}".format(integron_file))
if integrons:
integrons_report = results.integrons_report(integrons)
integrons_report.to_csv(integron_file,
sep="\t",
index=False,
na_rep="NA")
summary = results.summary(integrons_report)
summary_file = base_outfile + ".summary"
summary.to_csv(summary_file,
sep="\t",
na_rep="NA",
index=False,
columns=[
'ID_replicon', 'ID_integron', 'complete', 'In0',
'CALIN'
])
if config.gbk:
add_feature(replicon, integrons_report, protein_db,
config.distance_threshold)
SeqIO.write(
replicon,
os.path.join(config.result_dir, replicon.id + ".gbk"),
"genbank")
else:
with open(integron_file, "w") as out_f:
out_f.write("# No Integron found\n")
summary_file = None
except integron_finder.EmptyFileError as err:
_log.warning('############ Skip replicon {} ############'.format(
replicon.name))
integron_file = ''
summary_file = ''
#########################
# clean temporary files #
#########################
if not config.keep_tmp:
try:
shutil.rmtree(result_tmp_dir)
except Exception as err:
_log.warning("Cannot remove temporary results : '{} : {}'".format(
result_tmp_dir, str(err)))
return integron_file, summary_file